Timestamp 18-Jul-2025 22:46:01
pMakeSCFGModels: Looking for motifs in C:\Users\zirbel\Documents\JAR3D\Motifs\IL_3.98\mat
pMakeSCFGModels: Found 411 files
pMakeSCFGModels: Normalization variable is 1
pMakeSCFGModels: Parameter vector is 

Param =

     0     2     0     4   100     1     1     1   100     7     5

No transitions.mat file found, calculating transition probabilities
pCalculateTransitions:  processing IL_00225.13
  Columns 1 through 7

    {'> IL_00225.13  …'}    {'UGC*GA'}    {'> IL_00225.13  …'}    {'GGC*GC'}    {'> IL_00225.13  …'}    {'UGU*GA'}    {'> IL_00225.13  …'}

  Columns 8 through 14

    {'GGGCGC*GC'}    {'> IL_00225.13  …'}    {'UUUAGG*GA'}    {'> IL_00225.13  …'}    {'UUUAGG*GA'}    {'> IL_00225.13  …'}    {'GGC*GC'}

  Columns 15 through 20

    {'> IL_00225.13  …'}    {'GAGCGU*GC'}    {'> IL_00225.13  …'}    {'UUUGGG*GG'}    {'> IL_00225.13  …'}    {'AUAUGA*GU'}

  Columns 21 through 26

    {'> IL_00225.13  …'}    {'UUUGGG*GG'}    {'> IL_00225.13  …'}    {'AUAUGA*GU'}    {'> IL_00225.13  …'}    {'GGC*GC'}

  Columns 27 through 32

    {'> IL_00225.13  …'}    {'GGGCGC*GC'}    {'> IL_00225.13  …'}    {'GAGCGU*GC'}    {'> IL_00225.13  …'}    {'AAAUGU*GU'}

  Columns 33 through 38

    {'> IL_00225.13  …'}    {'GGGCGU*GC'}    {'> IL_00225.13  …'}    {'UGU*GA'}    {'> IL_00225.13  …'}    {'UUG*GA'}

  Columns 39 through 45

    {'> IL_00225.13  …'}    {'AUA*GU'}    {'> IL_00225.13  …'}    {'UGU*GA'}    {'> IL_00225.13  …'}    {'GUG*GC'}    {'> IL_00225.13  …'}

  Columns 46 through 52

    {'UUG*GA'}    {'> IL_00225.13  …'}    {'GUG*GC'}    {'> IL_00225.13  …'}    {'UUG*GA'}    {'> IL_00225.13  …'}    {'GUG*GC'}

  Columns 53 through 58

    {'> IL_00225.13  …'}    {'AAU*GU'}    {'> IL_00225.13  …'}    {'GCG*GU'}    {'> IL_00225.13  …'}    {'CGCGGU*GG'}

  Columns 59 through 65

    {'> IL_00225.13  …'}    {'GCG*GU'}    {'> IL_00225.13  …'}    {'GAU*GC'}    {'> IL_00225.13  …'}    {'UCG*GA'}    {'> IL_00225.13  …'}

  Columns 66 through 72

    {'UCG*GA'}    {'> IL_00225.13  …'}    {'GGU*GC'}    {'> IL_00225.13  …'}    {'UAUAGU*GA'}    {'> IL_00225.13  …'}    {'AGAUGC*GU'}

  Columns 73 through 78

    {'> IL_00225.13  …'}    {'UAUAGU*GA'}    {'> IL_00225.13  …'}    {'CUA*GG'}    {'> IL_00225.13  …'}    {'GAU*GC'}

  Columns 79 through 85

    {'> IL_00225.13  …'}    {'GGU*GC'}    {'> IL_00225.13  …'}    {'CGU*GG'}    {'> IL_00225.13  …'}    {'GGU*GC'}    {'> IL_00225.13  …'}

  Columns 86 through 92

    {'GGU*GC'}    {'> IL_00225.13  …'}    {'GGU*GC'}    {'> IL_00225.13  …'}    {'CGCGGC*GG'}    {'> IL_00225.13  …'}    {'GGC*GC'}

  Columns 93 through 98

    {'> IL_00225.13  …'}    {'GGU*GC'}    {'> IL_00225.13  …'}    {'CGCGGC*GG'}    {'> IL_00225.13  …'}    {'GGU*GC'}

pCalculateTransitions:  processing IL_00555.1
    {'> IL_00555.1  8P9A A 2520…'}    {'AUGAAGC*GGGU'}    {'> IL_00555.1  8CRE A 2498…'}    {'AUGAAGC*GGGU'}

pCalculateTransitions:  processing IL_00881.1
    {'> IL_00881.1  9DFE U 1415…'}    {'UGCA*AA'}    {'> IL_00881.1  5J7L U 1481…'}    {'UGCA*AG'}

pCalculateTransitions:  processing IL_00981.1
    {'> IL_00981.1  8P9A U 1694…'}    {'UUAAC*GGAAGA'}    {'> IL_00981.1  8CRE U 1690…'}    {'UUAAC*GGAAGA'}

pCalculateTransitions:  processing IL_01038.1
    {'> IL_01038.1  3OXE G   38 C   66'}    {'GCAAG*UGAAAC'}

pCalculateTransitions:  processing IL_01176.1
    {'> IL_01176.1  6FZ0 C   24 G   43'}    {'CGCCUU*AAAAG'}

pCalculateTransitions:  processing IL_01488.3
  Columns 1 through 6

    {'> IL_01488.3  6…'}    {'CGACGAUC*GGGAG'}    {'> IL_01488.3  6…'}    {'CAUCGAUC*GGGAG'}    {'> IL_01488.3  9…'}    {'CGUGGAUC*GGGAG'}

  Columns 7 through 12

    {'> IL_01488.3  1…'}    {'CAGAGAUG*CGGAG'}    {'> IL_01488.3  4…'}    {'CGAGGAUC*GGGAG'}    {'> IL_01488.3  4…'}    {'CUUUGAUC*GGGAG'}

  Columns 13 through 18

    {'> IL_01488.3  9…'}    {'CCAUGACG*CAGAG'}    {'> IL_01488.3  6…'}    {'CAUCGAUC*GGGAG'}    {'> IL_01488.3  5…'}    {'CGUAGAGA*UGUAG'}

  Columns 19 through 20

    {'> IL_01488.3  4…'}    {'CGAAGAAC*GGGAG'}

pCalculateTransitions:  processing IL_01994.1
    {'> IL_01994.1  6…'}    {'CGCGG*CUG'}    {'> IL_01994.1  5…'}    {'CGCGG*CUG'}    {'> IL_01994.1  7…'}    {'CGGUG*CUG'}

pCalculateTransitions:  processing IL_02203.1
    {'> IL_02203.1  4V9F A  965 U 1003'}    {'AUUG*CUGU'}

pCalculateTransitions:  processing IL_02349.4
  Columns 1 through 5

    {'> IL_02349.4  4…'}    {'GGGAGUAG*CGAGAC'}    {'> IL_02349.4  6…'}    {'GGGAGUAG*CGAGAC'}    {'> IL_02349.4  6…'}

  Column 6

    {'GGGAGUAG*CAAGAC'}

pCalculateTransitions:  processing IL_02555.1
  Columns 1 through 6

    {'> IL_02555.1  5…'}    {'UGC*AAG'}    {'> IL_02555.1  4…'}    {'UGC*AAG'}    {'> IL_02555.1  7…'}    {'UGC*AAG'}

  Columns 7 through 12

    {'> IL_02555.1  9…'}    {'UGC*AAG'}    {'> IL_02555.1  4…'}    {'UGC*AAG'}    {'> IL_02555.1  8…'}    {'UAU*AAG'}

  Columns 13 through 18

    {'> IL_02555.1  8…'}    {'UAU*AAG'}    {'> IL_02555.1  4…'}    {'CGC*AAG'}    {'> IL_02555.1  8…'}    {'CGCGAUC*UAG'}

pCalculateTransitions:  processing IL_03109.3
  Columns 1 through 6

    {'> IL_03109.3  8…'}    {'CCAAU*AG'}    {'> IL_03109.3  8…'}    {'CCAAU*AG'}    {'> IL_03109.3  5…'}    {'ACAAU*AU'}

  Columns 7 through 12

    {'> IL_03109.3  4…'}    {'GCAAU*AC'}    {'> IL_03109.3  4…'}    {'UGGCC*GG'}    {'> IL_03109.3  5…'}    {'UGACC*GG'}

pCalculateTransitions:  processing IL_03350.1
    {'> IL_03350.1  4…'}    {'CUCCCCACC*GAGG'}    {'> IL_03350.1  5…'}    {'CUACCCACC*GAGG'}    {'> IL_03350.1  4…'}    {'CUACCCACC*GAGG'}

pCalculateTransitions:  processing IL_04021.2
  Columns 1 through 5

    {'> IL_04021.2  4…'}    {'GUGGAUG*CUGAAAC'}    {'> IL_04021.2  5…'}    {'GUGGAUG*CUGAAAC'}    {'> IL_04021.2  7…'}

  Columns 6 through 10

    {'GUGGAUG*CUGAAAC'}    {'> IL_04021.2  8…'}    {'ACGGAUC*GUGAAAU'}    {'> IL_04021.2  9…'}    {'GUGGAUG*CUGAAAC'}

  Columns 11 through 14

    {'> IL_04021.2  8…'}    {'ACGGAUC*GUGAAAU'}    {'> IL_04021.2  4…'}    {'GUGGAUU*AUGAAAU'}

pCalculateTransitions:  processing IL_04073.1
    {'> IL_04073.1  8CRE A 1209 U 1244'}    {'AUAAGGAUUGA*UCUUGAUUU'}

pCalculateTransitions:  processing IL_04307.1
    {'> IL_04307.1  7VYX C   16 G   50'}    {'CCUCAGCCAU*ACCUUG'}

pCalculateTransitions:  processing IL_04332.3
    {'> IL_04332.3  7A0S C 1917…'}    {'CGAAAUUCCUUG*CCUG'}    {'> IL_04332.3  4V9F C 1975…'}    {'CGUAGUACCUUG*CUUG'}

pCalculateTransitions:  processing IL_04346.10
  Columns 1 through 5

    {'> IL_04346.10  …'}    {'GGAACUGC*UCAGUAC'}    {'> IL_04346.10  …'}    {'GGAACUGC*UAAGUAC'}    {'> IL_04346.10  …'}

  Columns 6 through 10

    {'AGAACUGC*UCAGUAU'}    {'> IL_04346.10  …'}    {'GGAACUGC*UCAGUAC'}    {'> IL_04346.10  …'}    {'GGAACCGCCAAGGCA…'}

  Columns 11 through 15

    {'> IL_04346.10  …'}    {'CGAACCCCCAAGCGA…'}    {'> IL_04346.10  …'}    {'CGAAACGCAAAGCGA…'}    {'> IL_04346.10  …'}

  Columns 16 through 20

    {'CGAAACUCAAAGCGA…'}    {'> IL_04346.10  …'}    {'CGAAACUCAAAGCGA…'}    {'> IL_04346.10  …'}    {'GGAACAGACAAGGCA…'}

  Columns 21 through 25

    {'> IL_04346.10  …'}    {'UGAAAUUUAAAGUAA…'}    {'> IL_04346.10  …'}    {'UGAAAUUUAAAGUAA…'}    {'> IL_04346.10  …'}

  Columns 26 through 30

    {'UGAAAUUUAAAGUAA…'}    {'> IL_04346.10  …'}    {'GGAACCGCCAAGGCA…'}    {'> IL_04346.10  …'}    {'UGAAAUCUAAAGUGA…'}

pCalculateTransitions:  processing IL_04600.1
    {'> IL_04600.1  5XWG U    9 A   15'}    {'UCGAAAA*UCGAAAA'}

pCalculateTransitions:  processing IL_04638.3
  Columns 1 through 5

    {'> IL_04638.3  9…'}    {'UUGAGCAA*GAUGAG'}    {'> IL_04638.3  7…'}    {'UUGAGCAA*GAUGAG'}    {'> IL_04638.3  4…'}

  Columns 6 through 10

    {'UUGAGCAA*GAUGAG'}    {'> IL_04638.3  5…'}    {'CUGAGCGA*GAUGAG'}    {'> IL_04638.3  4…'}    {'CUGACGGA*AAAGAG'}

pCalculateTransitions:  processing IL_04650.2
  Columns 1 through 6

    {'> IL_04650.2  6…'}    {'AACAACCCCG*CU'}    {'> IL_04650.2  7…'}    {'AACAACCCCG*CU'}    {'> IL_04650.2  7…'}    {'AACAUCCCCG*CU'}

  Columns 7 through 8

    {'> IL_04650.2  7…'}    {'AACAUCCCCG*CU'}

pCalculateTransitions:  processing IL_04736.1
    {'> IL_04736.1  3SIV C   40 G   46'}    {'CGCAUAG*CGCAUAG'}

pCalculateTransitions:  processing IL_04785.1
    {'> IL_04785.1  6DLR G   77…'}    {'GGAG*CAGGC'}    {'> IL_04785.1  7LIU C  708…'}    {'CCCG*CCCG'}

pCalculateTransitions:  processing IL_05192.4
    {'> IL_05192.4  3…'}    {'CAGGUA*UUGG'}    {'> IL_05192.4  7…'}    {'CCCCGG*GUCG'}    {'> IL_05192.4  7…'}    {'CAAGCG*AACG'}

pCalculateTransitions:  processing IL_05472.1
    {'> IL_05472.1  7JNH G   24 C   64'}    {'GUUUUUAACG*CUUUUC'}

pCalculateTransitions:  processing IL_06029.1
    {'> IL_06029.1  5J7L G 2123 C 2175'}    {'GGGAGGCCGACCUUGAA*AUACC'}

pCalculateTransitions:  processing IL_06136.2
  Columns 1 through 6

    {'> IL_06136.2  3…'}    {'GGGAAC*GGGAAC'}    {'> IL_06136.2  3…'}    {'GGGAAC*GGGAAC'}    {'> IL_06136.2  3…'}    {'GGGAAC*GGGAAC'}

  Columns 7 through 12

    {'> IL_06136.2  5…'}    {'CGGAUG*CGGAUG'}    {'> IL_06136.2  5…'}    {'CGGAUG*CGGAUG'}    {'> IL_06136.2  7…'}    {'GCGGAG*UGAAAC'}

pCalculateTransitions:  processing IL_06300.1
    {'> IL_06300.1  4WF9 U  889 A  978'}    {'UGAUG*UUAA'}

pCalculateTransitions:  processing IL_06549.2
  Columns 1 through 6

    {'> IL_06549.2  8…'}    {'GGG*UAAUC'}    {'> IL_06549.2  8…'}    {'GGG*UAAUC'}    {'> IL_06549.2  7…'}    {'GGA*UAACC'}

  Columns 7 through 12

    {'> IL_06549.2  5…'}    {'GGG*CAAUC'}    {'> IL_06549.2  9…'}    {'GGA*UAACC'}    {'> IL_06549.2  4…'}    {'GCG*CAAUC'}

pCalculateTransitions:  processing IL_06691.1
    {'> IL_06691.1  5J7L G 1124…'}    {'GUUGCGA*ACUC'}    {'> IL_06691.1  4V9F C 1004…'}    {'CAAACAAACGCCAGCGC*ACCG'}

pCalculateTransitions:  processing IL_07039.3
  Columns 1 through 6

    {'> IL_07039.3  4…'}    {'CGU*GG'}    {'> IL_07039.3  8…'}    {'CGU*GG'}    {'> IL_07039.3  8…'}    {'CGU*GG'}

  Columns 7 through 12

    {'> IL_07039.3  4…'}    {'CGU*GG'}    {'> IL_07039.3  9…'}    {'CGU*GG'}    {'> IL_07039.3  7…'}    {'CGU*GG'}

  Columns 13 through 18

    {'> IL_07039.3  4…'}    {'UGUGCU*CG'}    {'> IL_07039.3  8…'}    {'UGUGUU*UG'}    {'> IL_07039.3  8…'}    {'UGUGUU*UG'}

  Columns 19 through 24

    {'> IL_07039.3  5…'}    {'CGU*GG'}    {'> IL_07039.3  5…'}    {'UGUAGU*GA'}    {'> IL_07039.3  5…'}    {'AGAUAU*AU'}

  Columns 25 through 30

    {'> IL_07039.3  5…'}    {'AGAUAU*AU'}    {'> IL_07039.3  1…'}    {'AGU*AU'}    {'> IL_07039.3  5…'}    {'AGU*AU'}

  Columns 31 through 32

    {'> IL_07039.3  4…'}    {'AGU*AU'}

pCalculateTransitions:  processing IL_07171.1
    {'> IL_07171.1  4V9F U 2732 G 2750'}    {'UUAC*GUG'}

pCalculateTransitions:  processing IL_07173.1
    {'> IL_07173.1  8CRE G 1336 C 1360'}    {'GCUAUA*GUC'}

pCalculateTransitions:  processing IL_07469.2
    {'> IL_07469.2  8…'}    {'CAUAUA*AGCG'}    {'> IL_07469.2  8…'}    {'CAUAUA*AGCG'}    {'> IL_07469.2  8…'}    {'CGUUAG*UGCG'}

pCalculateTransitions:  processing IL_07785.1
  Columns 1 through 6

    {'> IL_07785.1  8…'}    {'UUU*AUA'}    {'> IL_07785.1  4…'}    {'AUA*UUU'}    {'> IL_07785.1  8…'}    {'UUA*UUG'}

  Columns 7 through 12

    {'> IL_07785.1  7…'}    {'AUG*CCU'}    {'> IL_07785.1  7…'}    {'UCG*CCG'}    {'> IL_07785.1  8…'}    {'UUG*CUG'}

  Columns 13 through 18

    {'> IL_07785.1  4…'}    {'UUG*UUG'}    {'> IL_07785.1  7…'}    {'ACU*ACU'}    {'> IL_07785.1  9…'}    {'AUG*CCU'}

  Columns 19 through 24

    {'> IL_07785.1  4…'}    {'UUG*UUG'}    {'> IL_07785.1  5…'}    {'AUG*CCU'}    {'> IL_07785.1  4…'}    {'AUG*CCU'}

  Columns 25 through 30

    {'> IL_07785.1  8…'}    {'UUA*UUG'}    {'> IL_07785.1  4…'}    {'GUG*CUC'}    {'> IL_07785.1  8…'}    {'GUUU*AUC'}

  Columns 31 through 36

    {'> IL_07785.1  4…'}    {'GAC*GCAC'}    {'> IL_07785.1  8…'}    {'UUAUC*GUG'}    {'> IL_07785.1  4…'}    {'CUC*GCGAG'}

  Columns 37 through 42

    {'> IL_07785.1  9…'}    {'CUC*GCGAG'}    {'> IL_07785.1  8…'}    {'CUC*GUGAG'}    {'> IL_07785.1  7…'}    {'GAG*CCAC'}

  Columns 43 through 48

    {'> IL_07785.1  5…'}    {'GUUG*CUC'}    {'> IL_07785.1  4…'}    {'GUU*AUAC'}    {'> IL_07785.1  8…'}    {'CUC*GUGAG'}

  Columns 49 through 54

    {'> IL_07785.1  7…'}    {'CUC*GCGAG'}    {'> IL_07785.1  5…'}    {'CUC*GCGAG'}    {'> IL_07785.1  8…'}    {'UUUG*CUG'}

  Columns 55 through 60

    {'> IL_07785.1  5…'}    {'UAC*GCCA'}    {'> IL_07785.1  4…'}    {'UUC*GUGAG'}    {'> IL_07785.1  7…'}    {'CAC*GCAG'}

  Columns 61 through 66

    {'> IL_07785.1  8…'}    {'UAA*UCGA'}    {'> IL_07785.1  8…'}    {'UAA*UCGA'}    {'> IL_07785.1  7…'}    {'CAG*CCCGG'}

pCalculateTransitions:  processing IL_08770.1
  Columns 1 through 6

    {'> IL_08770.1  2…'}    {'GAAG*CAC'}    {'> IL_08770.1  3…'}    {'GAAG*CAC'}    {'> IL_08770.1  7…'}    {'ACAG*CGU'}

  Columns 7 through 10

    {'> IL_08770.1  9…'}    {'CUG*CAG'}    {'> IL_08770.1  8…'}    {'ACA*UUU'}

pCalculateTransitions:  processing IL_09044.1
    {'> IL_09044.1  9DFE G 1526 C 1546'}    {'GGAAGU*GACAAC'}

pCalculateTransitions:  processing IL_09129.2
    {'> IL_09129.2  4LFB U 1247…'}    {'UACAAAG*CAAAAAG'}    {'> IL_09129.2  5J7L U 1247…'}    {'UACAAAG*CAUAAAG'}

pCalculateTransitions:  processing IL_09570.1
    {'> IL_09570.1  1YLS G  102 C  214'}    {'GAGCGGCC*GUGC'}

pCalculateTransitions:  processing IL_09705.15
  Columns 1 through 6

    {'> IL_09705.15  …'}    {'CGAG*CGAG'}    {'> IL_09705.15  …'}    {'CGAG*CGAG'}    {'> IL_09705.15  …'}    {'CGAG*CGAG'}

  Columns 7 through 12

    {'> IL_09705.15  …'}    {'CGAG*CGAG'}    {'> IL_09705.15  …'}    {'UGAC*GGAG'}    {'> IL_09705.15  …'}    {'AGAC*GGAU'}

  Columns 13 through 18

    {'> IL_09705.15  …'}    {'UGAC*GAAG'}    {'> IL_09705.15  …'}    {'UGAC*GGAG'}    {'> IL_09705.15  …'}    {'UGAU*AGAG'}

  Columns 19 through 24

    {'> IL_09705.15  …'}    {'UGAC*GAAG'}    {'> IL_09705.15  …'}    {'CGAG*CGAG'}    {'> IL_09705.15  …'}    {'CGAG*CGAG'}

  Columns 25 through 30

    {'> IL_09705.15  …'}    {'CGAC*GAAG'}    {'> IL_09705.15  …'}    {'CGAG*CGAG'}    {'> IL_09705.15  …'}    {'UAAC*GAAA'}

  Columns 31 through 36

    {'> IL_09705.15  …'}    {'UGAC*GGAG'}    {'> IL_09705.15  …'}    {'GGAC*GGAC'}    {'> IL_09705.15  …'}    {'CGAC*GAAG'}

  Columns 37 through 42

    {'> IL_09705.15  …'}    {'CAAC*GGCG'}    {'> IL_09705.15  …'}    {'CGAU*AGAG'}    {'> IL_09705.15  …'}    {'CCAC*GGCG'}

  Columns 43 through 48

    {'> IL_09705.15  …'}    {'CAAC*GGCG'}    {'> IL_09705.15  …'}    {'CGAU*AGAG'}    {'> IL_09705.15  …'}    {'UGAG*CAAA'}

  Columns 49 through 54

    {'> IL_09705.15  …'}    {'GAAG*CGAC'}    {'> IL_09705.15  …'}    {'UGAG*CAAA'}    {'> IL_09705.15  …'}    {'CCAC*GGAG'}

  Columns 55 through 60

    {'> IL_09705.15  …'}    {'AGAACG*CAAU'}    {'> IL_09705.15  …'}    {'AGAACG*CAAU'}    {'> IL_09705.15  …'}    {'CGAG*CGAG'}

  Columns 61 through 66

    {'> IL_09705.15  …'}    {'GGAG*UGAC'}    {'> IL_09705.15  …'}    {'AGAG*CGAU'}    {'> IL_09705.15  …'}    {'AGAG*CGAU'}

  Columns 67 through 68

    {'> IL_09705.15  …'}    {'CGAG*CGAG'}

pCalculateTransitions:  processing IL_09908.1
    {'> IL_09908.1  1U6B G  181 C  203'}    {'GGAGCAC*AAAC'}

pCalculateTransitions:  processing IL_09990.4
    {'> IL_09990.4  4V9F A 1465…'}    {'ACCG*ACU'}    {'> IL_09990.4  4WSM G   55…'}    {'GGCGGCCCG*CCC'}

pCalculateTransitions:  processing IL_10167.6
  Columns 1 through 6

    {'> IL_10167.6  3…'}    {'CGG*CGG'}    {'> IL_10167.6  3…'}    {'CGG*CGG'}    {'> IL_10167.6  3…'}    {'CGG*CGG'}

  Columns 7 through 12

    {'> IL_10167.6  3…'}    {'CGG*CGG'}    {'> IL_10167.6  3…'}    {'UGA*UGA'}    {'> IL_10167.6  3…'}    {'CGG*CGG'}

  Columns 13 through 18

    {'> IL_10167.6  3…'}    {'CGG*CGG'}    {'> IL_10167.6  3…'}    {'CGG*CGG'}    {'> IL_10167.6  3…'}    {'GGU*AGC'}

  Columns 19 through 24

    {'> IL_10167.6  3…'}    {'CGG*CGG'}    {'> IL_10167.6  4…'}    {'CGG*CGG'}    {'> IL_10167.6  4…'}    {'GGC*GGC'}

  Columns 25 through 30

    {'> IL_10167.6  2…'}    {'UGA*UGA'}    {'> IL_10167.6  4…'}    {'CGG*CGG'}    {'> IL_10167.6  4…'}    {'CGG*CGG'}

  Columns 31 through 36

    {'> IL_10167.6  4…'}    {'CGG*CGG'}    {'> IL_10167.6  3…'}    {'CGG*CGG'}    {'> IL_10167.6  4…'}    {'CGG*CGG'}

  Columns 37 through 42

    {'> IL_10167.6  4…'}    {'CGG*CGG'}    {'> IL_10167.6  3…'}    {'UGA*UGA'}    {'> IL_10167.6  2…'}    {'AGU*AAU'}

  Columns 43 through 48

    {'> IL_10167.6  6…'}    {'UGA*UGA'}    {'> IL_10167.6  4…'}    {'UGG*UGG'}    {'> IL_10167.6  5…'}    {'CGC*GGG'}

  Columns 49 through 54

    {'> IL_10167.6  4…'}    {'GGC*GGC'}    {'> IL_10167.6  4…'}    {'UGG*UGG'}    {'> IL_10167.6  4…'}    {'GGC*GGC'}

  Columns 55 through 60

    {'> IL_10167.6  4…'}    {'CAG*CAG'}    {'> IL_10167.6  3…'}    {'CGG*CGG'}    {'> IL_10167.6  4…'}    {'CAG*CAG'}

  Columns 61 through 66

    {'> IL_10167.6  4…'}    {'GGC*GGC'}    {'> IL_10167.6  6…'}    {'CGG*CGG'}    {'> IL_10167.6  4…'}    {'GGC*GGC'}

  Columns 67 through 72

    {'> IL_10167.6  4…'}    {'CGC*GGG'}    {'> IL_10167.6  2…'}    {'AGU*AAU'}    {'> IL_10167.6  3…'}    {'CGG*CGG'}

  Columns 73 through 78

    {'> IL_10167.6  4…'}    {'CAG*UGG'}    {'> IL_10167.6  5…'}    {'UGC*GGA'}    {'> IL_10167.6  8…'}    {'GGA*UAC'}

  Columns 79 through 84

    {'> IL_10167.6  8…'}    {'GGA*UAC'}    {'> IL_10167.6  5…'}    {'UGC*GGA'}    {'> IL_10167.6  8…'}    {'UGG*CGA'}

  Columns 85 through 90

    {'> IL_10167.6  7…'}    {'UGC*GGA'}    {'> IL_10167.6  8…'}    {'GUC*GUC'}    {'> IL_10167.6  4…'}    {'UGG*UGG'}

  Columns 91 through 96

    {'> IL_10167.6  4…'}    {'UGG*UGG'}    {'> IL_10167.6  8…'}    {'GUUU*GAC'}    {'> IL_10167.6  7…'}    {'CUU*ACG'}

  Columns 97 through 102

    {'> IL_10167.6  8…'}    {'GAU*AAUC'}    {'> IL_10167.6  8…'}    {'UGG*UGG'}    {'> IL_10167.6  8…'}    {'CAG*UAG'}

pCalculateTransitions:  processing IL_10389.1
    {'> IL_10389.1  4R4V G  724…'}    {'GACGC*AGC'}    {'> IL_10389.1  8D29 C    9…'}    {'CAGCCC*UUG'}

pCalculateTransitions:  processing IL_10484.1
    {'> IL_10484.1  6E7L U   10…'}    {'UUCG*UUCG'}    {'> IL_10484.1  3PDR U   28…'}    {'UGAG*UAAAG'}

pCalculateTransitions:  processing IL_10569.1
    {'> IL_10569.1  1HYS A  867…'}    {'AAA*UU'}    {'> IL_10569.1  4V84 C 6181…'}    {'CAG*CG'}

pCalculateTransitions:  processing IL_10796.1
    {'> IL_10796.1  4O41 U  306 G  409'}    {'UCG*UCG'}

pCalculateTransitions:  processing IL_11344.2
    {'> IL_11344.2  4LFB G 1255…'}    {'GAUGC*AAUC'}    {'> IL_11344.2  5J7L G 1255…'}    {'GAAGC*GACC'}

pCalculateTransitions:  processing IL_11399.2
    {'> IL_11399.2  9…'}    {'GGGUA*GGAC'}    {'> IL_11399.2  9…'}    {'GGGUGGGCAGGA*GGAC'}    {'> IL_11399.2  8…'}    {'CGCUA*AAAG'}

pCalculateTransitions:  processing IL_11415.1
    {'> IL_11415.1  8P9A U 1014 A 1036'}    {'UUCCG*UGA'}

pCalculateTransitions:  processing IL_12566.4
  Columns 1 through 6

    {'> IL_12566.4  5…'}    {'GAGAAC*GAC'}    {'> IL_12566.4  7…'}    {'GAGAAC*GAC'}    {'> IL_12566.4  9…'}    {'GAGAAC*GAC'}

  Columns 7 through 10

    {'> IL_12566.4  4…'}    {'GCGAAC*GAC'}    {'> IL_12566.4  4…'}    {'GAGCAAC*GGC'}

pCalculateTransitions:  processing IL_12697.1
    {'> IL_12697.1  8CRE U   37…'}    {'UCAAA*UGACAA'}    {'> IL_12697.1  8P9A U   37…'}    {'UCAAA*UGACAA'}

pCalculateTransitions:  processing IL_12745.1
    {'> IL_12745.1  4LFB G  148 C  174'}    {'GACAAC*GCUAAUC'}

pCalculateTransitions:  processing IL_13358.1
    {'> IL_13358.1  8P9A U  169 A  253'}    {'UGGGGUUC*UUUGUA'}

pCalculateTransitions:  processing IL_13394.1
    {'> IL_13394.1  5J7L G 1003 C 1037'}    {'GAAGUUAAUGUGCCU*GGGAAC'}

pCalculateTransitions:  processing IL_13404.2
  Columns 1 through 6

    {'> IL_13404.2  4…'}    {'UUCG*UUCG'}    {'> IL_13404.2  4…'}    {'UUCG*UUCG'}    {'> IL_13404.2  1…'}    {'UUCG*UUCG'}

  Columns 7 through 12

    {'> IL_13404.2  1…'}    {'UUCG*UUCG'}    {'> IL_13404.2  2…'}    {'UUCG*UUCG'}    {'> IL_13404.2  6…'}    {'UUCG*UUCG'}

  Columns 13 through 18

    {'> IL_13404.2  1…'}    {'UUCG*UUCG'}    {'> IL_13404.2  4…'}    {'UUCG*UUCG'}    {'> IL_13404.2  8…'}    {'AGAG*CUACU'}

  Columns 19 through 20

    {'> IL_13404.2  4…'}    {'GGCU*AUUC'}

pCalculateTransitions:  processing IL_13874.1
    {'> IL_13874.1  7OAX U    8 G   45'}    {'UGGAGGGG*CGGUCG'}

pCalculateTransitions:  processing IL_14177.2
    {'> IL_14177.2  4LFB C   47…'}    {'CCUAAG*UAG'}    {'> IL_14177.2  5J7L C   47…'}    {'CCUAAC*GGG'}

pCalculateTransitions:  processing IL_14368.1
  Columns 1 through 6

    {'> IL_14368.1  5…'}    {'CUAA*UG'}    {'> IL_14368.1  4…'}    {'CUAA*UG'}    {'> IL_14368.1  5…'}    {'CUAA*UG'}

  Columns 7 through 12

    {'> IL_14368.1  1…'}    {'CUAA*UG'}    {'> IL_14368.1  5…'}    {'CUAA*UG'}    {'> IL_14368.1  7…'}    {'GAGCA*UU'}

pCalculateTransitions:  processing IL_14688.1
  Columns 1 through 6

    {'> IL_14688.1  8…'}    {'GGU*AUAC'}    {'> IL_14688.1  7…'}    {'GGU*AUAC'}    {'> IL_14688.1  7…'}    {'UAC*GACG'}

  Columns 7 through 10

    {'> IL_14688.1  6…'}    {'ACC*GUU'}    {'> IL_14688.1  8…'}    {'UUU*ACA'}

pCalculateTransitions:  processing IL_15052.4
  Columns 1 through 6

    {'> IL_15052.4  3…'}    {'AAAC*GU'}    {'> IL_15052.4  3…'}    {'AAAC*GU'}    {'> IL_15052.4  5…'}    {'CAGC*GG'}

  Columns 7 through 12

    {'> IL_15052.4  4…'}    {'CCAGC*GG'}    {'> IL_15052.4  5…'}    {'UAAC*GA'}    {'> IL_15052.4  3…'}    {'UAAU*AA'}

  Columns 13 through 16

    {'> IL_15052.4  8…'}    {'GUAG*CC'}    {'> IL_15052.4  8…'}    {'GUAG*CC'}

pCalculateTransitions:  processing IL_15107.1
    {'> IL_15107.1  8D29 G    4 C   31'}    {'GAUACCAGCCC*UUGGCAGC'}

pCalculateTransitions:  processing IL_15218.1
    {'> IL_15218.1  7QR3 C    7…'}    {'CACAGCAGAAG*CG'}    {'> IL_15218.1  4PR6 C  107…'}    {'CAUGGUCCCAG*CG'}

pCalculateTransitions:  processing IL_15698.3
  Columns 1 through 6

    {'> IL_15698.3  5…'}    {'CAAC*GUG'}    {'> IL_15698.3  4…'}    {'CAAC*GUG'}    {'> IL_15698.3  4…'}    {'CAAC*GUG'}

  Columns 7 through 12

    {'> IL_15698.3  3…'}    {'CAAC*GUG'}    {'> IL_15698.3  4…'}    {'CAAC*GUG'}    {'> IL_15698.3  8…'}    {'GAUA*UGC'}

  Columns 13 through 18

    {'> IL_15698.3  8…'}    {'CAUG*UGG'}    {'> IL_15698.3  8…'}    {'GAUA*UGC'}    {'> IL_15698.3  5…'}    {'GAACAA*UAC'}

  Columns 19 through 20

    {'> IL_15698.3  8…'}    {'CAUG*UGG'}

pCalculateTransitions:  processing IL_15991.1
    {'> IL_15991.1  8CRE U  648 A  682'}    {'UGGCCGGUCGCGU*ACUGGACCCA'}

pCalculateTransitions:  processing IL_16218.2
    {'> IL_16218.2  8…'}    {'GUGGCG*AAUC'}    {'> IL_16218.2  8…'}    {'GUGGCG*AAUC'}    {'> IL_16218.2  7…'}    {'GUUGGC*ACCC'}

pCalculateTransitions:  processing IL_16386.4
  Columns 1 through 6

    {'> IL_16386.4  8…'}    {'CGC*GG'}    {'> IL_16386.4  8…'}    {'CGC*GG'}    {'> IL_16386.4  8…'}    {'CGC*GG'}

  Columns 7 through 8

    {'> IL_16386.4  8…'}    {'CGC*GG'}

pCalculateTransitions:  processing IL_16458.4
  Columns 1 through 6

    {'> IL_16458.4  7…'}    {'CUAGUAC*GGACCG'}    {'> IL_16458.4  5…'}    {'CUAGUAC*GGACCG'}    {'> IL_16458.4  9…'}    {'CUAGUAC*GGACCG'}

  Columns 7 through 10

    {'> IL_16458.4  4…'}    {'UUAGUAC*GGACCG'}    {'> IL_16458.4  4…'}    {'CCAGUAA*UGACCG'}

pCalculateTransitions:  processing IL_16665.1
    {'> IL_16665.1  5KPY G   47 C   75'}    {'GAAUUGUUG*CUAAC'}

pCalculateTransitions:  processing IL_17069.5
  Columns 1 through 5

    {'> IL_17069.5  5…'}    {'UGCAAACG*GACGUAUA'}    {'> IL_17069.5  9…'}    {'UGCGAACG*GAGGUAUA'}    {'> IL_17069.5  7…'}

  Columns 6 through 10

    {'UGCCAACG*GACGUAUA'}    {'> IL_17069.5  4…'}    {'UGCUAAAU*GAUGUAUA'}    {'> IL_17069.5  4…'}    {'CGCAAAUA*CUCGUACG'}

pCalculateTransitions:  processing IL_17136.7
  Columns 1 through 6

    {'> IL_17136.7  8…'}    {'CGAAG*CGUAG'}    {'> IL_17136.7  8…'}    {'CGAAG*CGUAG'}    {'> IL_17136.7  5…'}    {'CAAAC*GGUAG'}

  Columns 7 through 12

    {'> IL_17136.7  4…'}    {'CAAAC*GGUAG'}    {'> IL_17136.7  8…'}    {'UCAAG*CGUAG'}    {'> IL_17136.7  8…'}    {'UCAAG*CGUAG'}

  Columns 13 through 18

    {'> IL_17136.7  4…'}    {'UGAGG*UGUAG'}    {'> IL_17136.7  5…'}    {'UCAGG*CGCAG'}    {'> IL_17136.7  4…'}    {'UGAGG*CGUAG'}

  Columns 19 through 24

    {'> IL_17136.7  5…'}    {'CGAGG*CGUAG'}    {'> IL_17136.7  4…'}    {'UCAAC*GGUCG'}    {'> IL_17136.7  4…'}    {'CGAGG*CGCAG'}

  Columns 25 through 28

    {'> IL_17136.7  9…'}    {'UGAAG*CGUAG'}    {'> IL_17136.7  7…'}    {'UGAGG*CGCAG'}

pCalculateTransitions:  processing IL_17765.1
    {'> IL_17765.1  3D2V G   10 C   36'}    {'GGUGCUGAGA*AAGUC'}

pCalculateTransitions:  processing IL_17948.2
  Columns 1 through 6

    {'> IL_17948.2  5…'}    {'CCAAG*CGACG'}    {'> IL_17948.2  8…'}    {'UCAAG*CGACA'}    {'> IL_17948.2  8…'}    {'UCAAG*CGACA'}

  Columns 7 through 12

    {'> IL_17948.2  4…'}    {'CCAAG*CGACG'}    {'> IL_17948.2  7…'}    {'CCGAG*CGGCG'}    {'> IL_17948.2  9…'}    {'CCGAG*CGGCG'}

  Columns 13 through 18

    {'> IL_17948.2  4…'}    {'UCGAG*CGACA'}    {'> IL_17948.2  4…'}    {'GCAAG*CGACC'}    {'> IL_17948.2  5…'}    {'GCAAG*CAACC'}

  Columns 19 through 24

    {'> IL_17948.2  1…'}    {'GCAAC*GAAAC'}    {'> IL_17948.2  5…'}    {'GCAAG*CGACC'}    {'> IL_17948.2  7…'}    {'CUCAG*CAAGG'}

  Columns 25 through 26

    {'> IL_17948.2  6…'}    {'ACUUC*GUUUGU'}

pCalculateTransitions:  processing IL_17973.1
    {'> IL_17973.1  6UFG G   96 C  131'}    {'GCGGCAAGCGGGGUGG*CACC'}

pCalculateTransitions:  processing IL_18354.1
    {'> IL_18354.1  3NPQ G    7…'}    {'GGAGCGCUGC*GC'}    {'> IL_18354.1  7LYF G   73…'}    {'GGAGCUAAGCU*AC'}

pCalculateTransitions:  processing IL_18472.4
    {'> IL_18472.4  5…'}    {'GGUCCC*GAAAC'}    {'> IL_18472.4  9…'}    {'GGAACC*GAAAC'}    {'> IL_18472.4  7…'}    {'GGAACC*GAAAC'}

pCalculateTransitions:  processing IL_18487.1
    {'> IL_18487.1  8P9A G   21…'}    {'GAAAGCA*UUAAGC'}    {'> IL_18487.1  8OI5 G   21…'}    {'GAAAGCA*UUAAGC'}

pCalculateTransitions:  processing IL_19048.1
    {'> IL_19048.1  4WF9 A   20 U   59'}    {'AGGUCACA*UUAAGGU'}

pCalculateTransitions:  processing IL_19102.1
    {'> IL_19102.1  4PMI U   41…'}    {'UAUAU*AGG'}    {'> IL_19102.1  9IWF C   58…'}    {'CCCAG*CAG'}

pCalculateTransitions:  processing IL_19516.1
    {'> IL_19516.1  8T29 G   17 C   50'}    {'GGGGACCUACCCAC*GGAAC'}

pCalculateTransitions:  processing IL_19668.1
    {'> IL_19668.1  3E5C G   12…'}    {'GAUAG*AUGC'}    {'> IL_19668.1  6E8U U   30…'}    {'UGUGUAAGGAAA*GGAA'}

pCalculateTransitions:  processing IL_19852.1
    {'> IL_19852.1  8EYU A   16 U   38'}    {'AGGUGGGUGGU*AU'}

pCalculateTransitions:  processing IL_19897.3
    {'> IL_19897.3  7EOG U   14…'}    {'UGCCAAUCG*UA'}    {'> IL_19897.3  7SZU U   59…'}    {'UGUAUGCUAACCCAAUCG*UA'}

pCalculateTransitions:  processing IL_20031.1
    {'> IL_20031.1  8D29 A   10…'}    {'AGCC*CUU'}    {'> IL_20031.1  9E7E C   31…'}    {'CCCGCGGGG*CG'}

pCalculateTransitions:  processing IL_20047.1
    {'> IL_20047.1  8P9A C 2156…'}    {'CGAUGGU*GUUGACG'}    {'> IL_20047.1  8CRE U 2134…'}    {'UGAUGGU*GUUGACA'}

pCalculateTransitions:  processing IL_20245.1
    {'> IL_20245.1  5J7L G 2107 U 2182'}    {'GAUGUGUAGGAUAGGUG*CACCCUUU'}

pCalculateTransitions:  processing IL_20463.1
    {'> IL_20463.1  5DDP G   23 C   60'}    {'GAAGUAAUGAA*GCAACGC'}

pCalculateTransitions:  processing IL_21001.1
    {'> IL_21001.1  8…'}    {'UUUUUGC*GAAG'}    {'> IL_21001.1  8…'}    {'UUUUUGC*GAAG'}    {'> IL_21001.1  5…'}    {'AUUAGAUUAUAAGC*…'}

pCalculateTransitions:  processing IL_21173.1
    {'> IL_21173.1  7UQ6 G   30…'}    {'GUGGAACCC*GC'}    {'> IL_21173.1  7UZ0 G   43…'}    {'GUGGAACCC*GC'}

pCalculateTransitions:  processing IL_21200.1
  Columns 1 through 6

    {'> IL_21200.1  6…'}    {'CUAGCA*AGUG'}    {'> IL_21200.1  6…'}    {'CUAGCG*AGCG'}    {'> IL_21200.1  5…'}    {'CUAGCA*AGAG'}

  Columns 7 through 12

    {'> IL_21200.1  6…'}    {'CUAGCA*AGCG'}    {'> IL_21200.1  7…'}    {'CUAGCG*AGAG'}    {'> IL_21200.1  5…'}    {'CUAGCG*AGAG'}

pCalculateTransitions:  processing IL_21630.1
    {'> IL_21630.1  8Z8U G    6 C   36'}    {'GAGCCCAAC*GGCUAGAC'}

pCalculateTransitions:  processing IL_21667.1
    {'> IL_21667.1  8P9A U   64…'}    {'UAUAAG*UGAAA'}    {'> IL_21667.1  8CRE U   64…'}    {'UAUAAG*UGAAA'}

pCalculateTransitions:  processing IL_22373.1
  Columns 1 through 6

    {'> IL_22373.1  5…'}    {'GGUUC*GUC'}    {'> IL_22373.1  5…'}    {'GGUUC*GUC'}    {'> IL_22373.1  7…'}    {'GGUUC*GUC'}

  Columns 7 through 8

    {'> IL_22373.1  6…'}    {'GGUUC*GUC'}

pCalculateTransitions:  processing IL_22551.4
  Columns 1 through 6

    {'> IL_22551.4  8…'}    {'GCGC*AU'}    {'> IL_22551.4  8…'}    {'GCGC*AU'}    {'> IL_22551.4  4…'}    {'GCGC*AU'}

  Columns 7 through 12

    {'> IL_22551.4  9…'}    {'GCGC*AC'}    {'> IL_22551.4  7…'}    {'GCGC*AC'}    {'> IL_22551.4  5…'}    {'GCGC*AC'}

  Columns 13 through 18

    {'> IL_22551.4  4…'}    {'GCGC*AC'}    {'> IL_22551.4  8…'}    {'UCUAUUGU*UA'}    {'> IL_22551.4  3…'}    {'CUCGUCUAU*CUG'}

pCalculateTransitions:  processing IL_22564.1
    {'> IL_22564.1  8CRE G 1474…'}    {'GUAUAAGC*GAAAUC'}    {'> IL_22564.1  8P9A G 1488…'}    {'GUCUAAC*GUAAUC'}

pCalculateTransitions:  processing IL_22829.2
    {'> IL_22829.2  8…'}    {'AAUAAUG*CUAU'}    {'> IL_22829.2  8…'}    {'AAUAAUG*CUAU'}    {'> IL_22829.2  3…'}    {'GGGGUGC*GUCC'}

pCalculateTransitions:  processing IL_22854.4
  Columns 1 through 5

    {'> IL_22854.4  5…'}    {'GGAACUAGG*CUGUC'}    {'> IL_22854.4  4…'}    {'GGAACUCGG*CUGUC'}    {'> IL_22854.4  9…'}

  Columns 6 through 10

    {'GGAACUCUG*CUGUC'}    {'> IL_22854.4  4…'}    {'GGAAUUCGG*CUGUC'}    {'> IL_22854.4  7…'}    {'GGAACUUUG*CUGUC'}

  Columns 11 through 14

    {'> IL_22854.4  8…'}    {'GGAAGUCGG*CUGUC'}    {'> IL_22854.4  8…'}    {'GGAAGUCGG*CUGUC'}

pCalculateTransitions:  processing IL_23038.1
    {'> IL_23038.1  8P9A U 1702…'}    {'UUAUCAU*CUUAUG'}    {'> IL_23038.1  8CRE U 1698…'}    {'UUAUCAU*CUUAUG'}

pCalculateTransitions:  processing IL_23774.1
  Columns 1 through 6

    {'> IL_23774.1  4…'}    {'UGUACG*GUAG'}    {'> IL_23774.1  9…'}    {'UGGUGGUGAAGA*GAAG'}    {'> IL_23774.1  5…'}    {'CGAGU*GAAG'}

  Columns 7 through 12

    {'> IL_23774.1  8…'}    {'GGAGAGGCAUGU*GUAC'}    {'> IL_23774.1  8…'}    {'GGGGU*GCAC'}    {'> IL_23774.1  8…'}    {'GGGGU*GCAC'}

  Columns 13 through 18

    {'> IL_23774.1  2…'}    {'UGCAGACGUGAACC*…'}    {'> IL_23774.1  5…'}    {'UGUUCG*GUAG'}    {'> IL_23774.1  9…'}    {'UUUCCG*GUAG'}

  Columns 19 through 22

    {'> IL_23774.1  4…'}    {'UGUACG*GUAG'}    {'> IL_23774.1  7…'}    {'UCUCCG*GUAG'}

pCalculateTransitions:  processing IL_24134.1
    {'> IL_24134.1  2…'}    {'GGAGCGAG*AAAC'}    {'> IL_24134.1  2…'}    {'GGAGCGCG*AAAC'}    {'> IL_24134.1  1…'}    {'GGAGCGAG*AAAC'}

pCalculateTransitions:  processing IL_24254.1
    {'> IL_24254.1  1UN6 U   72 A  103'}    {'UUAGUAC*GGAAUA'}

pCalculateTransitions:  processing IL_24499.1
    {'> IL_24499.1  7ELQ A    6 U   41'}    {'AGAAGCGU*AAUU'}

pCalculateTransitions:  processing IL_25186.4
  Columns 1 through 6

    {'> IL_25186.4  7…'}    {'GACCC*GACAAC'}    {'> IL_25186.4  3…'}    {'CACCC*GACAAG'}    {'> IL_25186.4  3…'}    {'CACCC*GACAAG'}

  Columns 7 through 12

    {'> IL_25186.4  8…'}    {'GACCC*GACAAC'}    {'> IL_25186.4  7…'}    {'GACCC*GACAAC'}    {'> IL_25186.4  4…'}    {'CUAAG*UGAUGG'}

pCalculateTransitions:  processing IL_25412.1
    {'> IL_25412.1  1NTA C    7 G  114'}    {'CAUUUGG*CG'}

pCalculateTransitions:  processing IL_25463.1
    {'> IL_25463.1  8P9A C  977…'}    {'CGUAU*AAG'}    {'> IL_25463.1  1NTA A  105…'}    {'ACCACG*CU'}

pCalculateTransitions:  processing IL_25573.1
    {'> IL_25573.1  1F1T G    8 C   28'}    {'GACGGUA*AC'}

pCalculateTransitions:  processing IL_25872.4
  Columns 1 through 6

    {'> IL_25872.4  1…'}    {'GGGC*GGUAC'}    {'> IL_25872.4  1…'}    {'GGGC*GGUAC'}    {'> IL_25872.4  7…'}    {'CGGG*CGGG'}

  Columns 7 through 10

    {'> IL_25872.4  7…'}    {'GAGA*UGGU'}    {'> IL_25872.4  6…'}    {'AAAC*GCAU'}

pCalculateTransitions:  processing IL_26222.2
  Columns 1 through 6

    {'> IL_26222.2  4…'}    {'GCACU*AAAC'}    {'> IL_26222.2  7…'}    {'GCACU*AAAC'}    {'> IL_26222.2  9…'}    {'GCACU*AAAC'}

  Columns 7 through 12

    {'> IL_26222.2  5…'}    {'GCACU*AAAC'}    {'> IL_26222.2  8…'}    {'GCGAAU*AAAC'}    {'> IL_26222.2  8…'}    {'GCGAAU*AAAC'}

pCalculateTransitions:  processing IL_26307.2
  Columns 1 through 6

    {'> IL_26307.2  5…'}    {'CCAGUAG*CGAACG'}    {'> IL_26307.2  9…'}    {'UGAGUAG*CGAAAG'}    {'> IL_26307.2  4…'}    {'UUAGUAA*UGAACG'}

  Columns 7 through 12

    {'> IL_26307.2  8…'}    {'GUAGUAG*CGAAAC'}    {'> IL_26307.2  8…'}    {'GUAGUAG*CGAAAC'}    {'> IL_26307.2  4…'}    {'AUAGUAG*UGAACU'}

  Columns 13 through 18

    {'> IL_26307.2  4…'}    {'GGAGUAC*GGAAAU'}    {'> IL_26307.2  4…'}    {'AUAGUAC*GGAACU'}    {'> IL_26307.2  1…'}    {'UGAGUAU*AAAAAA'}

pCalculateTransitions:  processing IL_26598.1
  Columns 1 through 6

    {'> IL_26598.1  7…'}    {'GCGGCGUC*CC'}    {'> IL_26598.1  7…'}    {'GUGCCGUCCGAGCCU…'}    {'> IL_26598.1  7…'}    {'GCGGCGUC*CC'}

  Columns 7 through 10

    {'> IL_26598.1  7…'}    {'GUGCCGUCCGAGCCU…'}    {'> IL_26598.1  3…'}    {'GCGCCCAAAGGGAAA…'}

pCalculateTransitions:  processing IL_26685.1
    {'> IL_26685.1  3IGI G  128 U  238'}    {'GGUU*AU'}

pCalculateTransitions:  processing IL_26728.3
    {'> IL_26728.3  7EOG C    7…'}    {'CUGGU*GUCG'}    {'> IL_26728.3  7SZU C   52…'}    {'CUGGGUCGCUGU*GUCG'}

pCalculateTransitions:  processing IL_26793.1
  Columns 1 through 6

    {'> IL_26793.1  7…'}    {'GAG*CC'}    {'> IL_26793.1  8…'}    {'CUG*CG'}    {'> IL_26793.1  7…'}    {'AAG*CU'}

  Columns 7 through 12

    {'> IL_26793.1  5…'}    {'GAA*UC'}    {'> IL_26793.1  9…'}    {'CCU*AG'}    {'> IL_26793.1  5…'}    {'GAG*CC'}

  Columns 13 through 18

    {'> IL_26793.1  4…'}    {'UAG*CA'}    {'> IL_26793.1  7…'}    {'CCU*AG'}    {'> IL_26793.1  4…'}    {'CCU*AG'}

  Columns 19 through 24

    {'> IL_26793.1  5…'}    {'CCU*AG'}    {'> IL_26793.1  5…'}    {'AAG*CU'}    {'> IL_26793.1  8…'}    {'UAG*CA'}

  Columns 25 through 30

    {'> IL_26793.1  8…'}    {'UAG*CA'}    {'> IL_26793.1  7…'}    {'ACU*AU'}    {'> IL_26793.1  9…'}    {'GAG*CC'}

  Columns 31 through 32

    {'> IL_26793.1  5…'}    {'AAG*CU'}

pCalculateTransitions:  processing IL_27393.10
    {'> IL_27393.10  …'}    {'CUCCCCAC*GG'}    {'> IL_27393.10  …'}    {'CUACCCAC*GG'}    {'> IL_27393.10  …'}    {'CUACCCAC*GG'}

pCalculateTransitions:  processing IL_28026.3
    {'> IL_28026.3  4LFB G  409…'}    {'GGAAGAAG*UGUAAAC'}    {'> IL_28026.3  5J7L U  409…'}    {'UGAAGAAG*UGUAAAG'}

pCalculateTransitions:  processing IL_28037.2
  Columns 1 through 6

    {'> IL_28037.2  3…'}    {'GUC*GUC'}    {'> IL_28037.2  3…'}    {'GUC*GUC'}    {'> IL_28037.2  2…'}    {'GUC*GUC'}

  Columns 7 through 12

    {'> IL_28037.2  4…'}    {'AUC*GUU'}    {'> IL_28037.2  2…'}    {'GUC*GUC'}    {'> IL_28037.2  3…'}    {'GUC*GUC'}

  Columns 13 through 18

    {'> IL_28037.2  2…'}    {'GUC*GUC'}    {'> IL_28037.2  1…'}    {'AUC*GUU'}    {'> IL_28037.2  4…'}    {'GUC*GUC'}

  Columns 19 through 24

    {'> IL_28037.2  4…'}    {'GUC*GUC'}    {'> IL_28037.2  2…'}    {'GUC*GUC'}    {'> IL_28037.2  4…'}    {'AUC*GUU'}

  Columns 25 through 30

    {'> IL_28037.2  3…'}    {'GUC*GUC'}    {'> IL_28037.2  5…'}    {'AUC*GUU'}    {'> IL_28037.2  4…'}    {'CUG*CUG'}

  Columns 31 through 36

    {'> IL_28037.2  3…'}    {'AUG*CUU'}    {'> IL_28037.2  3…'}    {'GUC*GUC'}    {'> IL_28037.2  5…'}    {'UUC*GUA'}

  Columns 37 through 42

    {'> IL_28037.2  9…'}    {'ACC*GUU'}    {'> IL_28037.2  3…'}    {'GUC*GUC'}    {'> IL_28037.2  2…'}    {'GUC*GUC'}

  Columns 43 through 48

    {'> IL_28037.2  7…'}    {'AUG*CUU'}    {'> IL_28037.2  8…'}    {'AUU*AUU'}    {'> IL_28037.2  2…'}    {'GUC*GUC'}

  Columns 49 through 54

    {'> IL_28037.2  8…'}    {'AUU*AUU'}    {'> IL_28037.2  5…'}    {'GUC*GUC'}    {'> IL_28037.2  3…'}    {'GUC*GUC'}

  Columns 55 through 60

    {'> IL_28037.2  4…'}    {'GUC*GUC'}    {'> IL_28037.2  4…'}    {'GUG*CUC'}    {'> IL_28037.2  4…'}    {'CUC*GUG'}

  Columns 61 through 66

    {'> IL_28037.2  8…'}    {'AUA*UUU'}    {'> IL_28037.2  7…'}    {'GUG*CUC'}    {'> IL_28037.2  8…'}    {'ACU*AUU'}

  Columns 67 through 72

    {'> IL_28037.2  6…'}    {'CUG*CUG'}    {'> IL_28037.2  3…'}    {'GUC*GUC'}    {'> IL_28037.2  8…'}    {'AUA*UUU'}

  Columns 73 through 78

    {'> IL_28037.2  1…'}    {'GUC*GUC'}    {'> IL_28037.2  4…'}    {'GUC*GUC'}    {'> IL_28037.2  5…'}    {'CUG*CUG'}

  Columns 79 through 84

    {'> IL_28037.2  5…'}    {'GUC*GUC'}    {'> IL_28037.2  2…'}    {'GUC*GUC'}    {'> IL_28037.2  4…'}    {'CCG*CCG'}

  Columns 85 through 90

    {'> IL_28037.2  8…'}    {'GUA*UUC'}    {'> IL_28037.2  4…'}    {'GUG*CUC'}    {'> IL_28037.2  1…'}    {'AUG*CUU'}

  Columns 91 through 96

    {'> IL_28037.2  1…'}    {'AUG*CUU'}    {'> IL_28037.2  8…'}    {'AUU*ACU'}    {'> IL_28037.2  8…'}    {'AUA*UUU'}

  Columns 97 through 102

    {'> IL_28037.2  4…'}    {'GUC*GUC'}    {'> IL_28037.2  2…'}    {'GUC*GUC'}    {'> IL_28037.2  6…'}    {'UUA*UUA'}

  Columns 103 through 108

    {'> IL_28037.2  5…'}    {'CUG*UUG'}    {'> IL_28037.2  8…'}    {'AUG*UUU'}    {'> IL_28037.2  1…'}    {'GUC*GUC'}

  Columns 109 through 114

    {'> IL_28037.2  7…'}    {'CUG*UUG'}    {'> IL_28037.2  3…'}    {'AUG*CUU'}    {'> IL_28037.2  5…'}    {'GUC*GUC'}

  Columns 115 through 120

    {'> IL_28037.2  7…'}    {'AUG*CUU'}    {'> IL_28037.2  9…'}    {'CUG*UUG'}    {'> IL_28037.2  4…'}    {'CUG*CUG'}

  Columns 121 through 126

    {'> IL_28037.2  5…'}    {'CUG*CUG'}    {'> IL_28037.2  8…'}    {'AUG*UUU'}    {'> IL_28037.2  8…'}    {'AUG*CUU'}

  Columns 127 through 130

    {'> IL_28037.2  1…'}    {'AUC*GUU'}    {'> IL_28037.2  5…'}    {'UUU*AUG'}

pCalculateTransitions:  processing IL_28304.1
    {'> IL_28304.1  8P9A A 1224 U 1259'}    {'AUAAGGAUUG*CUUGAUUU'}

pCalculateTransitions:  processing IL_28564.1
    {'> IL_28564.1  6DTD U    8 A   31'}    {'UCUGU*AAA'}

pCalculateTransitions:  processing IL_28788.1
    {'> IL_28788.1  4ERD G  146 C  123'}    {'GGA*UCGAC'}

pCalculateTransitions:  processing IL_29198.2
  Columns 1 through 5

    {'> IL_29198.2  8…'}    {'GAGGUAA*UAAAUAU'}    {'> IL_29198.2  8…'}    {'GAGGUAA*UAAAUAU'}    {'> IL_29198.2  4…'}

  Columns 6 through 8

    {'GAGGUAG*CGAAUGC'}    {'> IL_29198.2  5…'}    {'GGGGUAG*CGAAUAC'}

pCalculateTransitions:  processing IL_29223.1
    {'> IL_29223.1  8P9A U  117…'}    {'UUAUUU*AUUCA'}    {'> IL_29223.1  8CRE U  117…'}    {'UUAUUU*AUUCA'}

pCalculateTransitions:  processing IL_29346.2
    {'> IL_29346.2  5…'}    {'GGGAG*UC'}    {'> IL_29346.2  4…'}    {'GGGAG*UC'}    {'> IL_29346.2  3…'}    {'CGAUUG*CG'}

pCalculateTransitions:  processing IL_29357.1
    {'> IL_29357.1  8DK7 G    4 C   31'}    {'GAUACCAGCC*CUUGGCAGC'}

pCalculateTransitions:  processing IL_29471.1
    {'> IL_29471.1  5J7L C 2806 G 2892'}    {'CUGAAG*CGUG'}

pCalculateTransitions:  processing IL_29826.1
    {'> IL_29826.1  4V9F U 1122 A 1242'}    {'UAAUCCUCUGAAGC*CAAAAUGAUCGGGA'}

pCalculateTransitions:  processing IL_30441.1
    {'> IL_30441.1  8GXB G    6 C   40'}    {'GUUACGUCCGAAAG*CAC'}

pCalculateTransitions:  processing IL_30730.1
    {'> IL_30730.1  7WIE U   17…'}    {'UUCAACUCG*CUA'}    {'> IL_30730.1  8XZL U   13…'}    {'UUCAACUCG*CUA'}

pCalculateTransitions:  processing IL_31084.1
    {'> IL_31084.1  1L9A U  181 A  216'}    {'UGAACCG*CAAAA'}

pCalculateTransitions:  processing IL_31462.6
  Columns 1 through 6

    {'> IL_31462.6  8…'}    {'AAG*CU'}    {'> IL_31462.6  1…'}    {'GAC*GC'}    {'> IL_31462.6  9…'}    {'AAG*CU'}

  Columns 7 through 12

    {'> IL_31462.6  1…'}    {'UAA*UA'}    {'> IL_31462.6  1…'}    {'GAC*GC'}    {'> IL_31462.6  5…'}    {'GAG*CC'}

  Columns 13 through 18

    {'> IL_31462.6  8…'}    {'GAC*GU'}    {'> IL_31462.6  3…'}    {'UAA*UA'}    {'> IL_31462.6  8…'}    {'CAG*CG'}

  Columns 19 through 24

    {'> IL_31462.6  9…'}    {'GAC*GC'}    {'> IL_31462.6  9…'}    {'UAU*AA'}    {'> IL_31462.6  5…'}    {'UAC*GA'}

  Columns 25 through 30

    {'> IL_31462.6  8…'}    {'UAG*CG'}    {'> IL_31462.6  8…'}    {'GAC*GU'}    {'> IL_31462.6  4…'}    {'UAC*GA'}

  Columns 31 through 36

    {'> IL_31462.6  8…'}    {'UAC*GA'}    {'> IL_31462.6  8…'}    {'UAC*GA'}    {'> IL_31462.6  4…'}    {'AAG*CU'}

  Columns 37 through 42

    {'> IL_31462.6  9…'}    {'UAC*GG'}    {'> IL_31462.6  4…'}    {'AAG*CU'}    {'> IL_31462.6  8…'}    {'UAC*GA'}

  Columns 43 through 48

    {'> IL_31462.6  1…'}    {'GAG*CC'}    {'> IL_31462.6  4…'}    {'CAG*CG'}    {'> IL_31462.6  8…'}    {'UAA*UG'}

  Columns 49 through 54

    {'> IL_31462.6  7…'}    {'CAU*AG'}    {'> IL_31462.6  7…'}    {'CAU*AG'}    {'> IL_31462.6  6…'}    {'GAG*CC'}

  Columns 55 through 60

    {'> IL_31462.6  4…'}    {'AAG*CU'}    {'> IL_31462.6  8…'}    {'CAG*UG'}    {'> IL_31462.6  5…'}    {'GAC*GC'}

  Columns 61 through 66

    {'> IL_31462.6  4…'}    {'GAG*CC'}    {'> IL_31462.6  9…'}    {'GAC*GC'}    {'> IL_31462.6  3…'}    {'CAG*CG'}

  Columns 67 through 72

    {'> IL_31462.6  4…'}    {'GAC*GC'}    {'> IL_31462.6  5…'}    {'CAG*CG'}    {'> IL_31462.6  1…'}    {'UAA*UA'}

  Columns 73 through 78

    {'> IL_31462.6  9…'}    {'GAC*GC'}    {'> IL_31462.6  2…'}    {'GAA*UC'}    {'> IL_31462.6  1…'}    {'GAC*GC'}

  Columns 79 through 84

    {'> IL_31462.6  1…'}    {'GAC*GC'}    {'> IL_31462.6  8…'}    {'GAG*CC'}    {'> IL_31462.6  8…'}    {'GAG*CC'}

  Columns 85 through 90

    {'> IL_31462.6  6…'}    {'GAA*UC'}    {'> IL_31462.6  2…'}    {'GAG*CC'}    {'> IL_31462.6  8…'}    {'AAU*AU'}

  Columns 91 through 96

    {'> IL_31462.6  8…'}    {'CAG*CG'}    {'> IL_31462.6  8…'}    {'GAG*CU'}    {'> IL_31462.6  1…'}    {'UAC*GA'}

  Columns 97 through 102

    {'> IL_31462.6  4…'}    {'CAG*CG'}    {'> IL_31462.6  4…'}    {'AAG*CU'}    {'> IL_31462.6  8…'}    {'GAU*AC'}

  Columns 103 through 108

    {'> IL_31462.6  5…'}    {'GAU*AC'}    {'> IL_31462.6  8…'}    {'AAU*AU'}    {'> IL_31462.6  8…'}    {'GAG*CU'}

  Columns 109 through 114

    {'> IL_31462.6  3…'}    {'GAG*CC'}    {'> IL_31462.6  4…'}    {'UAG*CA'}    {'> IL_31462.6  7…'}    {'GAU*GC'}

  Columns 115 through 120

    {'> IL_31462.6  7…'}    {'GAU*AC'}    {'> IL_31462.6  8…'}    {'CAG*CG'}    {'> IL_31462.6  7…'}    {'GAC*GC'}

  Columns 121 through 126

    {'> IL_31462.6  1…'}    {'GAA*UC'}    {'> IL_31462.6  3…'}    {'AAC*GU'}    {'> IL_31462.6  5…'}    {'GAU*GC'}

  Columns 127 through 132

    {'> IL_31462.6  9…'}    {'GAG*CC'}    {'> IL_31462.6  4…'}    {'GAC*GC'}    {'> IL_31462.6  4…'}    {'GAU*GC'}

  Columns 133 through 138

    {'> IL_31462.6  9…'}    {'GAC*GC'}    {'> IL_31462.6  8…'}    {'AAU*AU'}    {'> IL_31462.6  4…'}    {'CAG*CG'}

  Columns 139 through 144

    {'> IL_31462.6  8…'}    {'GAU*AC'}    {'> IL_31462.6  6…'}    {'CAC*GG'}    {'> IL_31462.6  6…'}    {'GAG*CC'}

  Columns 145 through 150

    {'> IL_31462.6  4…'}    {'GAA*UC'}    {'> IL_31462.6  8…'}    {'UAG*CG'}    {'> IL_31462.6  7…'}    {'GAG*CC'}

  Columns 151 through 156

    {'> IL_31462.6  7…'}    {'GAC*GC'}    {'> IL_31462.6  4…'}    {'GAU*AC'}    {'> IL_31462.6  4…'}    {'CAC*GG'}

  Columns 157 through 162

    {'> IL_31462.6  5…'}    {'GAC*GC'}    {'> IL_31462.6  3…'}    {'GAC*GU'}    {'> IL_31462.6  2…'}    {'CAG*CG'}

  Columns 163 through 168

    {'> IL_31462.6  4…'}    {'CAU*AG'}    {'> IL_31462.6  7…'}    {'UAC*GG'}    {'> IL_31462.6  8…'}    {'UAG*CG'}

  Columns 169 through 174

    {'> IL_31462.6  8…'}    {'GAU*AC'}    {'> IL_31462.6  8…'}    {'CAG*CG'}    {'> IL_31462.6  6…'}    {'GAG*CC'}

  Columns 175 through 180

    {'> IL_31462.6  8…'}    {'CAG*CG'}    {'> IL_31462.6  1…'}    {'GAG*CC'}    {'> IL_31462.6  9…'}    {'GAG*CC'}

  Columns 181 through 186

    {'> IL_31462.6  8…'}    {'GAC*GC'}    {'> IL_31462.6  7…'}    {'UAG*CA'}    {'> IL_31462.6  4…'}    {'CAC*GG'}

  Columns 187 through 192

    {'> IL_31462.6  8…'}    {'AAG*CU'}    {'> IL_31462.6  8…'}    {'AAG*CU'}    {'> IL_31462.6  8…'}    {'UAG*CG'}

  Columns 193 through 198

    {'> IL_31462.6  5…'}    {'GAG*CC'}    {'> IL_31462.6  9…'}    {'UAG*CG'}    {'> IL_31462.6  9…'}    {'UAU*AA'}

  Columns 199 through 204

    {'> IL_31462.6  7…'}    {'UAC*GG'}    {'> IL_31462.6  8…'}    {'AAU*AU'}    {'> IL_31462.6  8…'}    {'GAG*CC'}

  Columns 205 through 210

    {'> IL_31462.6  3…'}    {'GAA*UC'}    {'> IL_31462.6  4…'}    {'CAG*CG'}    {'> IL_31462.6  2…'}    {'UAG*CG'}

  Columns 211 through 216

    {'> IL_31462.6  5…'}    {'CAG*CG'}    {'> IL_31462.6  5…'}    {'CAA*UG'}    {'> IL_31462.6  8…'}    {'GAC*GC'}

  Columns 217 through 222

    {'> IL_31462.6  7…'}    {'UAG*CA'}    {'> IL_31462.6  8…'}    {'CAG*CG'}    {'> IL_31462.6  8…'}    {'CAG*CG'}

  Columns 223 through 228

    {'> IL_31462.6  9…'}    {'CAG*CG'}    {'> IL_31462.6  8…'}    {'GAC*GC'}    {'> IL_31462.6  5…'}    {'CAU*AG'}

  Columns 229 through 234

    {'> IL_31462.6  4…'}    {'GAG*CC'}    {'> IL_31462.6  5…'}    {'GAG*CC'}    {'> IL_31462.6  4…'}    {'GAC*GU'}

  Columns 235 through 240

    {'> IL_31462.6  4…'}    {'GAG*CC'}    {'> IL_31462.6  2…'}    {'CAG*CG'}    {'> IL_31462.6  4…'}    {'UAC*GA'}

  Columns 241 through 246

    {'> IL_31462.6  8…'}    {'CAC*GG'}    {'> IL_31462.6  5…'}    {'UAG*CG'}    {'> IL_31462.6  4…'}    {'CAG*CG'}

  Columns 247 through 252

    {'> IL_31462.6  4…'}    {'UAG*CG'}    {'> IL_31462.6  5…'}    {'UAG*CG'}    {'> IL_31462.6  7…'}    {'UAC*GG'}

  Columns 253 through 258

    {'> IL_31462.6  9…'}    {'CAG*CG'}    {'> IL_31462.6  4…'}    {'UAG*CA'}    {'> IL_31462.6  4…'}    {'CAG*CG'}

  Columns 259 through 260

    {'> IL_31462.6  7…'}    {'UAC*GG'}

pCalculateTransitions:  processing IL_31504.1
    {'> IL_31504.1  4V9F G  487 C  515'}    {'GUACCGAGGCGAA*AUAGAGC'}

pCalculateTransitions:  processing IL_31531.3
  Columns 1 through 6

    {'> IL_31531.3  2…'}    {'CACG*AAG'}    {'> IL_31531.3  2…'}    {'CACG*AAG'}    {'> IL_31531.3  4…'}    {'CGUGCGAAA*AAG'}

  Columns 7 through 12

    {'> IL_31531.3  4…'}    {'CACG*AAG'}    {'> IL_31531.3  1…'}    {'CACACGAAG*AAG'}    {'> IL_31531.3  4…'}    {'CACG*AAG'}

  Columns 13 through 18

    {'> IL_31531.3  3…'}    {'CACG*AAG'}    {'> IL_31531.3  1…'}    {'CACACGAAG*AAG'}    {'> IL_31531.3  7…'}    {'GGCG*GAC'}

  Columns 19 through 24

    {'> IL_31531.3  1…'}    {'CACACGAAG*AAG'}    {'> IL_31531.3  5…'}    {'GAGAGCAAU*AAC'}    {'> IL_31531.3  4…'}    {'GAGU*GAC'}

  Columns 25 through 26

    {'> IL_31531.3  3…'}    {'GAGU*AAC'}

pCalculateTransitions:  processing IL_31558.1
    {'> IL_31558.1  6JXM C   35 G   53'}    {'CGAAG*UGGG'}

pCalculateTransitions:  processing IL_31561.1
    {'> IL_31561.1  4LFB G  450 C  483'}    {'GAAACCG*ACUGAC'}

pCalculateTransitions:  processing IL_31737.3
  Columns 1 through 6

    {'> IL_31737.3  2…'}    {'GUCG*UC'}    {'> IL_31737.3  2…'}    {'GUCG*UC'}    {'> IL_31737.3  2…'}    {'CUA*AG'}

  Columns 7 through 12

    {'> IL_31737.3  7…'}    {'UACG*AG'}    {'> IL_31737.3  8…'}    {'CCGCCGCC*CG'}    {'> IL_31737.3  2…'}    {'GAAGC*AC'}

  Columns 13 through 18

    {'> IL_31737.3  4…'}    {'GAUG*AC'}    {'> IL_31737.3  4…'}    {'CACACGAG*AG'}    {'> IL_31737.3  4…'}    {'CACACGAG*AG'}

  Columns 19 through 24

    {'> IL_31737.3  8…'}    {'GACGCAGCGC*GC'}    {'> IL_31737.3  3…'}    {'GAAGC*AC'}    {'> IL_31737.3  8…'}    {'UCUUGU*AA'}

pCalculateTransitions:  processing IL_31915.1
  Columns 1 through 5

    {'> IL_31915.1  3…'}    {'GUUUUUCG*UUUUUAUC'}    {'> IL_31915.1  6…'}    {'GUUUUUCG*UUUUUAUC'}    {'> IL_31915.1  7…'}

  Column 6

    {'GGUUUUCUUUUGGCA…'}

pCalculateTransitions:  processing IL_32016.1
    {'> IL_32016.1  4V9F U 1587 G 1608'}    {'UGGAAG*CAGGAAG'}

pCalculateTransitions:  processing IL_32056.1
    {'> IL_32056.1  5…'}    {'GUGCAGCAUAG*CC'}    {'> IL_32056.1  3…'}    {'GCGUAGGAUAG*CC'}    {'> IL_32056.1  1…'}    {'GCGUAGGAUAG*CC'}

pCalculateTransitions:  processing IL_33141.1
    {'> IL_33141.1  8DK7 C    8 G   27'}    {'CCAGCCC*UUGG'}

pCalculateTransitions:  processing IL_33323.1
    {'> IL_33323.1  8D28 C    9…'}    {'CAGCCC*UUG'}    {'> IL_33323.1  5J7L C  440…'}    {'CAGCAG*AAG'}

pCalculateTransitions:  processing IL_33623.1
    {'> IL_33623.1  5T83 C   69 G   89'}    {'CACGGAAG*CUGG'}

pCalculateTransitions:  processing IL_33711.1
    {'> IL_33711.1  6N2V A   45…'}    {'AACAUACUC*GU'}    {'> IL_33711.1  6CB3 G   38…'}    {'GUCAAUUCG*CC'}

pCalculateTransitions:  processing IL_33761.2
    {'> IL_33761.2  4…'}    {'UGAC*GG'}    {'> IL_33761.2  1…'}    {'GUC*GC'}    {'> IL_33761.2  8…'}    {'CAC*GG'}

pCalculateTransitions:  processing IL_33886.1
    {'> IL_33886.1  4V9F C  245…'}    {'CGAAGC*AAUGUG'}    {'> IL_33886.1  1NTA C   15…'}    {'CUUCUA*CCACGG'}

pCalculateTransitions:  processing IL_34470.3
    {'> IL_34470.3  3DIL G   22…'}    {'GAUGAGUAG*UGAAAGGC'}    {'> IL_34470.3  3D0U G   19…'}    {'GAUGAGUAG*UGAAAGGC'}

pCalculateTransitions:  processing IL_34737.1
    {'> IL_34737.1  8CRE C  973 G 1100'}    {'CGUAUC*GAAG'}

pCalculateTransitions:  processing IL_34739.3
  Columns 1 through 5

    {'> IL_34739.3  4…'}    {'GAAACAAUACAGAGA…'}    {'> IL_34739.3  6…'}    {'GAAACAAUACAGAGA…'}    {'> IL_34739.3  5…'}

  Column 6

    {'GAAACAAUACAGAGA…'}

pCalculateTransitions:  processing IL_34822.1
    {'> IL_34822.1  3PDR A   60…'}    {'AAAAAU*GCCAAU'}    {'> IL_34822.1  4V9F C 1578…'}    {'CCAACU*ACGAACG'}

pCalculateTransitions:  processing IL_36516.3
  Columns 1 through 6

    {'> IL_36516.3  7…'}    {'ACUAA*UCU'}    {'> IL_36516.3  7…'}    {'ACUAA*UCU'}    {'> IL_36516.3  6…'}    {'ACUAA*GCU'}

  Columns 7 through 11

    {'> IL_36516.3  6…'}    {'GACAGCUAGGG*AUC'}    {'> IL_36516.3  6…'}    {'GACAGCUUGGG*UUC'}    {'> IL_36516.3  4…'}

  Columns 12 through 14

    {'CAGACGUGACA*GUG'}    {'> IL_36516.3  8…'}    {'CGCGCGUAAGA*AUG'}

pCalculateTransitions:  processing IL_36729.1
    {'> IL_36729.1  8Z8U G    6 C   36'}    {'GAGCCCAAC*GGCUAGAC'}

pCalculateTransitions:  processing IL_37015.1
    {'> IL_37015.1  5J7L G   81 C  105'}    {'GUAAGCGU*UAUAAC'}

pCalculateTransitions:  processing IL_37603.1
    {'> IL_37603.1  3SUX G    6 C   96'}    {'GAGCAUCU*CGC'}

pCalculateTransitions:  processing IL_37752.1
    {'> IL_37752.1  8EPK A    5 U   26'}    {'ACUAUACCG*CUGCCU'}

pCalculateTransitions:  processing IL_38186.6
  Columns 1 through 6

    {'> IL_38186.6  4…'}    {'CGUAAAG*CG'}    {'> IL_38186.6  5…'}    {'CGUAAAG*CG'}    {'> IL_38186.6  8…'}    {'GUUAAAA*UC'}

  Columns 7 through 8

    {'> IL_38186.6  8…'}    {'GUUAAAA*UC'}

pCalculateTransitions:  processing IL_38394.1
    {'> IL_38394.1  8F4O U   20…'}    {'UGCUGAGA*AA'}    {'> IL_38394.1  7TZS U   20…'}    {'UGCUGAGA*AA'}

pCalculateTransitions:  processing IL_38507.2
  Columns 1 through 6

    {'> IL_38507.2  5…'}    {'CUAAG*CGAAG'}    {'> IL_38507.2  4…'}    {'CUAAG*CGAAG'}    {'> IL_38507.2  9…'}    {'CUAAG*CGAAG'}

  Columns 7 through 12

    {'> IL_38507.2  7…'}    {'CUAAG*CGAAG'}    {'> IL_38507.2  4…'}    {'UUAAG*CGAGA'}    {'> IL_38507.2  8…'}    {'AUUAU*AGAAU'}

  Columns 13 through 18

    {'> IL_38507.2  8…'}    {'AUUAU*AGAAU'}    {'> IL_38507.2  5…'}    {'CUAAG*CGAAG'}    {'> IL_38507.2  8…'}    {'UUAAA*UUAUA'}

  Columns 19 through 24

    {'> IL_38507.2  9…'}    {'CUAAG*CGAUG'}    {'> IL_38507.2  9…'}    {'CUAAG*CGAAG'}    {'> IL_38507.2  8…'}    {'UUAAG*CUAUA'}

  Columns 25 through 30

    {'> IL_38507.2  8…'}    {'CUAAG*CGAAAG'}    {'> IL_38507.2  8…'}    {'CUAAG*CGAAAG'}    {'> IL_38507.2  7…'}    {'CUAAA*UGAUG'}

  Columns 31 through 32

    {'> IL_38507.2  9…'}    {'CUGAC*GGUG'}

pCalculateTransitions:  processing IL_38634.5
    {'> IL_38634.5  3K0J U   59…'}    {'UGAUC*GCGUA'}    {'> IL_38634.5  3D2V U   47…'}    {'UGAAC*GCGCA'}

pCalculateTransitions:  processing IL_38862.4
  Columns 1 through 6

    {'> IL_38862.4  9…'}    {'UGUAG*CGAAG'}    {'> IL_38862.4  7…'}    {'UGUAG*CGAAG'}    {'> IL_38862.4  4…'}    {'GGUAG*CAAAC'}

  Columns 7 through 10

    {'> IL_38862.4  5…'}    {'UGUAG*UGAGG'}    {'> IL_38862.4  2…'}    {'CGUAU*AAAAG'}

pCalculateTransitions:  processing IL_38969.1
    {'> IL_38969.1  6N5P C   36 G   99'}    {'CGCUUUUUG*CAG'}

pCalculateTransitions:  processing IL_41203.4
  Columns 1 through 6

    {'> IL_41203.4  9…'}    {'CCCCCAAG*CG'}    {'> IL_41203.4  4…'}    {'UCCCCAAG*CA'}    {'> IL_41203.4  5…'}    {'UCCCAAAG*CA'}

  Columns 7 through 12

    {'> IL_41203.4  8…'}    {'UGCCGGAA*UA'}    {'> IL_41203.4  8…'}    {'UGCCGGAA*UA'}    {'> IL_41203.4  4…'}    {'UCCCAAAA*UA'}

  Columns 13 through 18

    {'> IL_41203.4  7…'}    {'UCCCUAAA*UA'}    {'> IL_41203.4  5…'}    {'CGGCUAAC*GG'}    {'> IL_41203.4  8…'}    {'AGGGCAAG*CU'}

  Columns 19 through 22

    {'> IL_41203.4  8…'}    {'AGGGCAAG*CU'}    {'> IL_41203.4  4…'}    {'CGGCCAAC*GG'}

pCalculateTransitions:  processing IL_41344.1
    {'> IL_41344.1  4PDQ G   16…'}    {'GAAG*CAC'}    {'> IL_41344.1  3PDR U  159…'}    {'UCUA*UUAG'}

pCalculateTransitions:  processing IL_41756.4
  Columns 1 through 5

    {'> IL_41756.4  8…'}    {'GGAGUAUG*UGAAAC'}    {'> IL_41756.4  8…'}    {'GGAGUAUG*UGAAAC'}    {'> IL_41756.4  4…'}

  Columns 6 through 8

    {'GGAGUACG*UGAAAC'}    {'> IL_41756.4  5…'}    {'GGAGUACG*UAAAAC'}

pCalculateTransitions:  processing IL_41853.1
    {'> IL_41853.1  4V9F C 1521 G 1665'}    {'CAGUGAAAG*CGAG'}

pCalculateTransitions:  processing IL_42032.1
    {'> IL_42032.1  4LFB C 1158…'}    {'CUGCGAG*GAAG'}    {'> IL_42032.1  5J7L C 1158…'}    {'CUGCGAG*GAAG'}

pCalculateTransitions:  processing IL_42218.2
  Columns 1 through 5

    {'> IL_42218.2  5…'}    {'CGAAAUUCCUUG*CCUG'}    {'> IL_42218.2  9…'}    {'CGAAAUUCCUUG*CCUG'}    {'> IL_42218.2  4…'}

  Columns 6 through 10

    {'CGAAAUUCCUUG*CCCG'}    {'> IL_42218.2  8…'}    {'CCAAAUGCCUCG*CGCG'}    {'> IL_42218.2  8…'}    {'CCAAAUGCCUCG*CGCG'}

pCalculateTransitions:  processing IL_42231.1
    {'> IL_42231.1  8CRE U 3149…'}    {'UACGAAUAAG*CGCUGGA'}    {'> IL_42231.1  8P9A U 3179…'}    {'UACGAAUAAG*CGCUGAA'}

pCalculateTransitions:  processing IL_42314.1
    {'> IL_42314.1  4KQY U   52 A   71'}    {'UGUAA*UGA'}

pCalculateTransitions:  processing IL_42626.2
  Columns 1 through 6

    {'> IL_42626.2  4…'}    {'CC*GUCG'}    {'> IL_42626.2  8…'}    {'CU*AACG'}    {'> IL_42626.2  9…'}    {'CU*AUAAG'}

  Columns 7 through 12

    {'> IL_42626.2  8…'}    {'CU*AACG'}    {'> IL_42626.2  7…'}    {'CU*ACAUG'}    {'> IL_42626.2  8…'}    {'CU*AACG'}

  Columns 13 through 18

    {'> IL_42626.2  3…'}    {'UA*UACG'}    {'> IL_42626.2  9…'}    {'CG*CACG'}    {'> IL_42626.2  7…'}    {'CG*CACG'}

  Columns 19 through 24

    {'> IL_42626.2  5…'}    {'UU*ACUG'}    {'> IL_42626.2  4…'}    {'UU*AUAG'}    {'> IL_42626.2  4…'}    {'CA*UACG'}

  Columns 25 through 28

    {'> IL_42626.2  5…'}    {'CA*UACG'}    {'> IL_42626.2  1…'}    {'UG*CACG'}

pCalculateTransitions:  processing IL_42771.1
  Columns 1 through 6

    {'> IL_42771.1  6…'}    {'UUA*UUA'}    {'> IL_42771.1  6…'}    {'UUA*UUA'}    {'> IL_42771.1  6…'}    {'UUA*UUA'}

  Columns 7 through 12

    {'> IL_42771.1  4…'}    {'AAA*UU'}    {'> IL_42771.1  4…'}    {'CAG*CG'}    {'> IL_42771.1  8…'}    {'CAA*UG'}

pCalculateTransitions:  processing IL_42778.1
    {'> IL_42778.1  6QIT C    2 G    7'}    {'CAGCAG*CAGCAG'}

pCalculateTransitions:  processing IL_42997.3
  Columns 1 through 6

    {'> IL_42997.3  7…'}    {'CAG*CAG'}    {'> IL_42997.3  4…'}    {'GAC*GAC'}    {'> IL_42997.3  8…'}    {'AAG*CAU'}

  Columns 7 through 12

    {'> IL_42997.3  3…'}    {'CAG*CAG'}    {'> IL_42997.3  3…'}    {'CAG*CAG'}    {'> IL_42997.3  8…'}    {'AAG*CAU'}

  Columns 13 through 18

    {'> IL_42997.3  9…'}    {'UGU*AUA'}    {'> IL_42997.3  7…'}    {'CAG*CAG'}    {'> IL_42997.3  7…'}    {'UAU*ACA'}

  Columns 19 through 24

    {'> IL_42997.3  2…'}    {'UUA*UUA'}    {'> IL_42997.3  5…'}    {'CGU*AGUG'}    {'> IL_42997.3  7…'}    {'CGU*AGUG'}

  Columns 25 through 30

    {'> IL_42997.3  4…'}    {'CGC*GACG'}    {'> IL_42997.3  8…'}    {'CGU*AGUG'}    {'> IL_42997.3  8…'}    {'CGU*AGUG'}

  Columns 31 through 36

    {'> IL_42997.3  4…'}    {'CGU*AGUG'}    {'> IL_42997.3  9…'}    {'CGU*AGUG'}    {'> IL_42997.3  5…'}    {'CGA*UCG'}

  Columns 37 through 40

    {'> IL_42997.3  7…'}    {'GUG*CUC'}    {'> IL_42997.3  4…'}    {'CUG*CUG'}

pCalculateTransitions:  processing IL_43140.1
    {'> IL_43140.1  7OAX C   16 G   39'}    {'CGUGGUUGG*GUG'}

pCalculateTransitions:  processing IL_43467.1
    {'> IL_43467.1  1U6B A  134 U  173'}    {'AGACGGCACCC*GAAGGCAU'}

pCalculateTransitions:  processing IL_43547.1
  Columns 1 through 5

    {'> IL_43547.1  6…'}    {'GAAGAACGCC*AGUA…'}    {'> IL_43547.1  6…'}    {'GAAGAACGCC*AGUA…'}    {'> IL_43547.1  6…'}

  Column 6

    {'GAAGAACGUC*AGUA…'}

pCalculateTransitions:  processing IL_43622.1
    {'> IL_43622.1  8P9A G 3328…'}    {'GUAUU*AAGC'}    {'> IL_43622.1  8CRE G 3293…'}    {'GUAUU*AAGC'}

pCalculateTransitions:  processing IL_43644.1
    {'> IL_43644.1  5J7L C 2103…'}    {'CCUU*AAUG'}    {'> IL_43644.1  5EW4 C   14…'}    {'CCCG*CCCG'}

pCalculateTransitions:  processing IL_43858.1
    {'> IL_43858.1  8P9A G  531…'}    {'GAAUGUAGU*AUUAUAGC'}    {'> IL_43858.1  8CRE G  527…'}    {'GAAUGUGGU*GUUAUAGC'}

pCalculateTransitions:  processing IL_44325.1
    {'> IL_44325.1  5LYS C   33 G   78'}    {'CACGC*AG'}

pCalculateTransitions:  processing IL_44438.1
    {'> IL_44438.1  8F4O U   59 A   80'}    {'UGAUCU*AGCGUA'}

pCalculateTransitions:  processing IL_44465.1
  Columns 1 through 6

    {'> IL_44465.1  1…'}    {'UGA*UGA'}    {'> IL_44465.1  1…'}    {'UGA*UGA'}    {'> IL_44465.1  8…'}    {'CGG*CGG'}

  Columns 7 through 12

    {'> IL_44465.1  8…'}    {'UGU*AGA'}    {'> IL_44465.1  5…'}    {'UGG*UGA'}    {'> IL_44465.1  7…'}    {'CAA*UGG'}

  Columns 13 through 18

    {'> IL_44465.1  5…'}    {'UGG*UGA'}    {'> IL_44465.1  7…'}    {'GUA*UUC'}    {'> IL_44465.1  9…'}    {'GGAG*CGC'}

pCalculateTransitions:  processing IL_44624.1
    {'> IL_44624.1  7TZS G   18…'}    {'GGUGCUGAGA*AAUAC'}    {'> IL_44624.1  8F4O G   18…'}    {'GGUGCUGAGA*AAUAC'}

pCalculateTransitions:  processing IL_44874.1
    {'> IL_44874.1  3NDB C  192 G  226'}    {'CGAACCC*GUAG'}

pCalculateTransitions:  processing IL_45444.1
    {'> IL_45444.1  1NUV C   22…'}    {'CCGAGC*GGAG'}    {'> IL_45444.1  1NUV C   22…'}    {'CCGAGC*GGAG'}

pCalculateTransitions:  processing IL_45896.1
    {'> IL_45896.1  3IAB C   64 G   99'}    {'CAGUAAUAUG*CUUACAAAAUGG'}

pCalculateTransitions:  processing IL_46086.1
    {'> IL_46086.1  9DFE U 1481 G 1510'}    {'UGCAACA*AG'}

pCalculateTransitions:  processing IL_46112.1
    {'> IL_46112.1  4Y1M A   44 U   64'}    {'AACAUUUUC*GU'}

pCalculateTransitions:  processing IL_46174.3
  Columns 1 through 5

    {'> IL_46174.3  8…'}    {'UAUCAAUU*UCAACG'}    {'> IL_46174.3  8…'}    {'UAUCAAUU*UCAACG'}    {'> IL_46174.3  5…'}

  Columns 6 through 10

    {'GAUUAGCG*ACGAUC'}    {'> IL_46174.3  4…'}    {'CAUCAGCG*ACGACG'}    {'> IL_46174.3  3…'}    {'UAAGACAGCA*AUGACG'}

pCalculateTransitions:  processing IL_46387.1
    {'> IL_46387.1  2…'}    {'AUGCC*AAU'}    {'> IL_46387.1  9…'}    {'ACCCAUCUUGU*UCU'}    {'> IL_46387.1  7…'}    {'CGCGG*UGG'}

pCalculateTransitions:  processing IL_47074.2
  Columns 1 through 6

    {'> IL_47074.2  4…'}    {'UAGU*AG'}    {'> IL_47074.2  5…'}    {'UAGU*AG'}    {'> IL_47074.2  4…'}    {'AAGC*GU'}

  Columns 7 through 8

    {'> IL_47074.2  8…'}    {'UUUCGA*UG'}

pCalculateTransitions:  processing IL_47078.3
  Columns 1 through 6

    {'> IL_47078.3  5…'}    {'GCAUUC*CC'}    {'> IL_47078.3  4…'}    {'GCAUUC*CC'}    {'> IL_47078.3  5…'}    {'ACAUACAGAC*AU'}

  Columns 7 through 8

    {'> IL_47078.3  4…'}    {'ACAUACAGAC*AU'}

pCalculateTransitions:  processing IL_47087.1
    {'> IL_47087.1  3P59 G   51 C  112'}    {'GGAACUAC*GCC'}

pCalculateTransitions:  processing IL_47108.1
    {'> IL_47108.1  5Y7M U    8 G   44'}    {'UUAAUGA*AAG'}

pCalculateTransitions:  processing IL_47346.2
  Columns 1 through 6

    {'> IL_47346.2  8…'}    {'CGUAAC*GGAUAAG'}    {'> IL_47346.2  8…'}    {'CGUAAC*GGAUAAG'}    {'> IL_47346.2  4…'}    {'CGUACC*GAAGAAG'}

  Columns 7 through 12

    {'> IL_47346.2  9…'}    {'CGUAAC*GGAGAAG'}    {'> IL_47346.2  7…'}    {'CGUAAC*GAAGAAG'}    {'> IL_47346.2  5…'}    {'CGUAAC*GGAGAAG'}

  Columns 13 through 14

    {'> IL_47346.2  4…'}    {'CGUAAC*GGAGAAG'}

pCalculateTransitions:  processing IL_47972.1
    {'> IL_47972.1  5J7L C  269 G  370'}    {'CAGCG*AUG'}

pCalculateTransitions:  processing IL_48076.6
  Columns 1 through 6

    {'> IL_48076.6  9…'}    {'GGC*AC'}    {'> IL_48076.6  5…'}    {'GGC*AC'}    {'> IL_48076.6  4…'}    {'GAU*AC'}

  Columns 7 through 12

    {'> IL_48076.6  7…'}    {'GGC*AC'}    {'> IL_48076.6  4…'}    {'GGC*AC'}    {'> IL_48076.6  8…'}    {'GAGCGU*GC'}

  Columns 13 through 18

    {'> IL_48076.6  3…'}    {'UCG*UA'}    {'> IL_48076.6  7…'}    {'GGGCAU*AC'}    {'> IL_48076.6  1…'}    {'UGUAAU*AA'}

  Columns 19 through 24

    {'> IL_48076.6  5…'}    {'UGUAAU*AA'}    {'> IL_48076.6  9…'}    {'GGGCCU*CC'}    {'> IL_48076.6  8…'}    {'GGU*UC'}

  Columns 25 through 30

    {'> IL_48076.6  5…'}    {'GGC*GC'}    {'> IL_48076.6  4…'}    {'UGC*AA'}    {'> IL_48076.6  1…'}    {'GGU*AC'}

  Columns 31 through 36

    {'> IL_48076.6  5…'}    {'UGUAAC*AA'}    {'> IL_48076.6  1…'}    {'UGC*AA'}    {'> IL_48076.6  1…'}    {'UGC*AA'}

  Columns 37 through 42

    {'> IL_48076.6  4…'}    {'GCGCGG*GC'}    {'> IL_48076.6  3…'}    {'GGC*UC'}    {'> IL_48076.6  7…'}    {'CGCGAC*AG'}

  Columns 43 through 48

    {'> IL_48076.6  9…'}    {'GGU*AC'}    {'> IL_48076.6  9…'}    {'CGCGAC*AG'}    {'> IL_48076.6  5…'}    {'CGU*GG'}

  Columns 49 through 54

    {'> IL_48076.6  7…'}    {'GGGCAC*AC'}    {'> IL_48076.6  5…'}    {'GGC*GC'}    {'> IL_48076.6  4…'}    {'CGCGAC*AG'}

  Columns 55 through 60

    {'> IL_48076.6  9…'}    {'UCG*CA'}    {'> IL_48076.6  9…'}    {'UCG*CA'}    {'> IL_48076.6  1…'}    {'GGC*CC'}

  Columns 61 through 66

    {'> IL_48076.6  1…'}    {'GGC*CC'}    {'> IL_48076.6  4…'}    {'GGC*CC'}    {'> IL_48076.6  9…'}    {'UGUAGU*GA'}

  Columns 67 through 72

    {'> IL_48076.6  4…'}    {'UUUAAAA*AA'}    {'> IL_48076.6  7…'}    {'UGUAGU*GA'}    {'> IL_48076.6  4…'}    {'UGUAUU*UA'}

  Columns 73 through 78

    {'> IL_48076.6  4…'}    {'GCGCAG*AC'}    {'> IL_48076.6  5…'}    {'UCUAAAG*AA'}    {'> IL_48076.6  5…'}    {'GCGCAG*AC'}

  Columns 79 through 82

    {'> IL_48076.6  3…'}    {'GAU*GU'}    {'> IL_48076.6  8…'}    {'GGU*UUC'}

pCalculateTransitions:  processing IL_48444.6
  Columns 1 through 6

    {'> IL_48444.6  1…'}    {'UAAG*CAGUA'}    {'> IL_48444.6  1…'}    {'UAAG*CAGUA'}    {'> IL_48444.6  7…'}    {'CUAC*GGUCAG'}

  Columns 7 through 8

    {'> IL_48444.6  6…'}    {'CGAU*AGAAG'}

pCalculateTransitions:  processing IL_49061.1
  Columns 1 through 6

    {'> IL_49061.1  4…'}    {'CGGGAG*CAG'}    {'> IL_49061.1  5…'}    {'CGGAAA*UGG'}    {'> IL_49061.1  1…'}    {'CCGAG*CAG'}

  Columns 7 through 12

    {'> IL_49061.1  4…'}    {'GGAAG*CAC'}    {'> IL_49061.1  4…'}    {'GGAUC*GAC'}    {'> IL_49061.1  8…'}    {'UCUGUGA*UGG'}

pCalculateTransitions:  processing IL_49612.1
    {'> IL_49612.1  5J7L C 1051…'}    {'CGGCAU*AUGG'}    {'> IL_49612.1  8CRE G 1415…'}    {'GUCUGUGA*UGGC'}

pCalculateTransitions:  processing IL_49714.1
    {'> IL_49714.1  3TZR G   52 C  111'}    {'GAACUAC*GC'}

pCalculateTransitions:  processing IL_49751.4
  Columns 1 through 6

    {'> IL_49751.4  8…'}    {'CUCCU*ACUUG'}    {'> IL_49751.4  8…'}    {'CUCCU*ACUUG'}    {'> IL_49751.4  8…'}    {'CUUUG*CUCUG'}

  Columns 7 through 12

    {'> IL_49751.4  8…'}    {'CUCUG*CUUUG'}    {'> IL_49751.4  8…'}    {'CUCUG*CUUUG'}    {'> IL_49751.4  8…'}    {'CUUUG*CUCUG'}

  Columns 13 through 18

    {'> IL_49751.4  8…'}    {'CCUUG*CUCCG'}    {'> IL_49751.4  5…'}    {'UUCUA*UUCUA'}    {'> IL_49751.4  7…'}    {'GUGCC*GACUU'}

  Columns 19 through 24

    {'> IL_49751.4  7…'}    {'UUAUC*GGAUG'}    {'> IL_49751.4  8…'}    {'GCGUG*CACAC'}    {'> IL_49751.4  8…'}    {'GAUAC*GCAGC'}

  Columns 25 through 30

    {'> IL_49751.4  4…'}    {'GGAAC*GGAAU'}    {'> IL_49751.4  5…'}    {'GGAAU*AGAAU'}    {'> IL_49751.4  4…'}    {'CCCAG*UAGGG'}

  Columns 31 through 32

    {'> IL_49751.4  5…'}    {'CCCCAG*CCCCG'}

pCalculateTransitions:  processing IL_49767.8
  Columns 1 through 6

    {'> IL_49767.8  7…'}    {'GAUAAC*GGAAGC'}    {'> IL_49767.8  9…'}    {'GAUAAC*GGAAGC'}    {'> IL_49767.8  4…'}    {'GGUAAG*CGAAAC'}

  Columns 7 through 12

    {'> IL_49767.8  4…'}    {'GAUAAG*UGAAGC'}    {'> IL_49767.8  5…'}    {'GAUAAG*CGAAAC'}    {'> IL_49767.8  7…'}    {'UCUAAA*UGAUGG'}

pCalculateTransitions:  processing IL_49867.1
    {'> IL_49867.1  1YLS G  211 C  235'}    {'GUGCCGGC*AAUACUC'}

pCalculateTransitions:  processing IL_49971.1
    {'> IL_49971.1  1NTA C    5 G  115'}    {'CGCAUUUGG*CGG'}

pCalculateTransitions:  processing IL_50694.7
  Columns 1 through 6

    {'> IL_50694.7  4…'}    {'GAUG*AC'}    {'> IL_50694.7  5…'}    {'GAUG*AC'}    {'> IL_50694.7  1…'}    {'GAUG*AC'}

  Columns 7 through 12

    {'> IL_50694.7  1…'}    {'GAUG*AC'}    {'> IL_50694.7  1…'}    {'GAUG*AC'}    {'> IL_50694.7  9…'}    {'UCUAAGGG*AA'}

  Columns 13 through 18

    {'> IL_50694.7  6…'}    {'GGCG*AC'}    {'> IL_50694.7  5…'}    {'UCUAAGGG*AA'}    {'> IL_50694.7  8…'}    {'AGCA*UU'}

  Columns 19 through 24

    {'> IL_50694.7  4…'}    {'GGCG*UC'}    {'> IL_50694.7  4…'}    {'GGCG*UC'}    {'> IL_50694.7  9…'}    {'ACAUUGGG*UU'}

  Columns 25 through 30

    {'> IL_50694.7  4…'}    {'UCUAAGGG*AA'}    {'> IL_50694.7  4…'}    {'UCUAAGGG*AA'}    {'> IL_50694.7  4…'}    {'GGCG*UC'}

  Columns 31 through 36

    {'> IL_50694.7  8…'}    {'UCUAAGGG*AA'}    {'> IL_50694.7  7…'}    {'UCUAAGGG*AA'}    {'> IL_50694.7  4…'}    {'ACAUUUGU*UU'}

  Columns 37 through 42

    {'> IL_50694.7  4…'}    {'UGUAAGCG*AA'}    {'> IL_50694.7  8…'}    {'UCUAAGGG*AA'}    {'> IL_50694.7  5…'}    {'ACAUUGGG*UU'}

  Columns 43 through 48

    {'> IL_50694.7  4…'}    {'ACAUUGGG*UU'}    {'> IL_50694.7  7…'}    {'ACAUUGGG*UU'}    {'> IL_50694.7  1…'}    {'GGGCUUCU*UC'}

  Columns 49 through 54

    {'> IL_50694.7  7…'}    {'AGAUUGUG*UU'}    {'> IL_50694.7  3…'}    {'GGGCUACA*UC'}    {'> IL_50694.7  3…'}    {'GGGCUACA*UC'}

pCalculateTransitions:  processing IL_50715.3
  Columns 1 through 5

    {'> IL_50715.3  4…'}    {'GGAAAAGCGAAAAUG…'}    {'> IL_50715.3  5…'}    {'GGGAAACGGAAGAUG…'}    {'> IL_50715.3  7…'}

  Columns 6 through 8

    {'GGUUAAGCGAAAAUG…'}    {'> IL_50715.3  9…'}    {'GGUAAAGCGAAAAUG…'}

pCalculateTransitions:  processing IL_50730.2
  Columns 1 through 6

    {'> IL_50730.2  8…'}    {'UGAAU*AGGAA'}    {'> IL_50730.2  8…'}    {'UGAAU*AGGAA'}    {'> IL_50730.2  5…'}    {'UGAGG*UGGAG'}

  Columns 7 through 12

    {'> IL_50730.2  4…'}    {'UGAAG*UGGAG'}    {'> IL_50730.2  9…'}    {'UGAAG*UGGAG'}    {'> IL_50730.2  4…'}    {'UGAAG*UGGAA'}

  Columns 13 through 18

    {'> IL_50730.2  8…'}    {'UGAAG*UGGAG'}    {'> IL_50730.2  5…'}    {'UGAAG*UGGAG'}    {'> IL_50730.2  3…'}    {'CAAAC*GGACG'}

  Columns 19 through 24

    {'> IL_50730.2  9…'}    {'CGAAC*GGGAG'}    {'> IL_50730.2  4…'}    {'UAAAC*GGGCG'}    {'> IL_50730.2  3…'}    {'CAAAC*GGACG'}

  Columns 25 through 30

    {'> IL_50730.2  8…'}    {'UGAAG*UGGAG'}    {'> IL_50730.2  2…'}    {'CGAAG*CGGAG'}    {'> IL_50730.2  2…'}    {'CGAAG*CGGAG'}

  Columns 31 through 36

    {'> IL_50730.2  3…'}    {'CUAAC*GGACG'}    {'> IL_50730.2  8…'}    {'AGAAG*CGGAU'}    {'> IL_50730.2  8…'}    {'AGAAU*AGGAU'}

  Columns 37 through 38

    {'> IL_50730.2  7…'}    {'CGAAA*UGGAG'}

pCalculateTransitions:  processing IL_51191.1
    {'> IL_51191.1  6OL3 A   35 U  128'}    {'AAGCAG*GUGU'}

pCalculateTransitions:  processing IL_51265.3
  Columns 1 through 6

    {'> IL_51265.3  3…'}    {'CAAUGAG*UGAG'}    {'> IL_51265.3  3…'}    {'CAAUGAG*UGAG'}    {'> IL_51265.3  3…'}    {'CAAUGAG*UGAG'}

  Columns 7 through 12

    {'> IL_51265.3  4…'}    {'CGAUGAG*CGAG'}    {'> IL_51265.3  2…'}    {'CAAUGAG*CGAG'}    {'> IL_51265.3  1…'}    {'CAAUGAG*CGAG'}

pCalculateTransitions:  processing IL_51387.2
  Columns 1 through 6

    {'> IL_51387.2  9…'}    {'GGUG*CUC'}    {'> IL_51387.2  8…'}    {'GGUU*AUC'}    {'> IL_51387.2  7…'}    {'GGUG*CUC'}

  Columns 7 through 12

    {'> IL_51387.2  8…'}    {'GGUU*AUC'}    {'> IL_51387.2  4…'}    {'GUUG*CUC'}    {'> IL_51387.2  8…'}    {'UUUUC*GUA'}

  Columns 13 through 18

    {'> IL_51387.2  8…'}    {'UUUUC*GUA'}    {'> IL_51387.2  5…'}    {'GAGUG*CUC'}    {'> IL_51387.2  1…'}    {'GAGUG*CUC'}

  Columns 19 through 24

    {'> IL_51387.2  8…'}    {'UUUUU*GUG'}    {'> IL_51387.2  8…'}    {'UUUUU*GUG'}    {'> IL_51387.2  8…'}    {'GAGUG*CUC'}

  Columns 25 through 30

    {'> IL_51387.2  4…'}    {'GGCUU*GUC'}    {'> IL_51387.2  8…'}    {'GAGUG*CUC'}    {'> IL_51387.2  9…'}    {'GGUUU*AUC'}

  Columns 31 through 36

    {'> IL_51387.2  4…'}    {'GGUUU*AUC'}    {'> IL_51387.2  7…'}    {'GGUUU*AUC'}    {'> IL_51387.2  5…'}    {'UGUUU*AUA'}

  Columns 37 through 40

    {'> IL_51387.2  4…'}    {'CAAC*GCG'}    {'> IL_51387.2  3…'}    {'CUCC*GUG'}

pCalculateTransitions:  processing IL_51454.3
  Columns 1 through 6

    {'> IL_51454.3  6…'}    {'CGC*UG'}    {'> IL_51454.3  8…'}    {'AAU*UU'}    {'> IL_51454.3  7…'}    {'CGC*UG'}

  Columns 7 through 12

    {'> IL_51454.3  5…'}    {'CGC*UG'}    {'> IL_51454.3  8…'}    {'AAU*UU'}    {'> IL_51454.3  8…'}    {'CGCGUUC*UUG'}

  Columns 13 through 18

    {'> IL_51454.3  4…'}    {'GAU*CC'}    {'> IL_51454.3  2…'}    {'CAU*AG'}    {'> IL_51454.3  7…'}    {'GAU*CC'}

  Columns 19 through 24

    {'> IL_51454.3  5…'}    {'GAU*CC'}    {'> IL_51454.3  8…'}    {'CGCGUC*UG'}    {'> IL_51454.3  4…'}    {'GAU*CC'}

  Columns 25 through 30

    {'> IL_51454.3  9…'}    {'GAU*CC'}    {'> IL_51454.3  9…'}    {'GGU*AC'}    {'> IL_51454.3  4…'}    {'GGC*AC'}

  Columns 31 through 36

    {'> IL_51454.3  5…'}    {'CGCGAC*AG'}    {'> IL_51454.3  8…'}    {'CGCGUC*UG'}    {'> IL_51454.3  8…'}    {'UUUACA*CA'}

  Columns 37 through 42

    {'> IL_51454.3  6…'}    {'UCG*AA'}    {'> IL_51454.3  8…'}    {'UUUACA*CA'}    {'> IL_51454.3  8…'}    {'GAU*CC'}

  Columns 43 through 48

    {'> IL_51454.3  5…'}    {'GGC*AC'}    {'> IL_51454.3  8…'}    {'GGC*AC'}    {'> IL_51454.3  7…'}    {'AGAUCC*CU'}

  Columns 49 through 54

    {'> IL_51454.3  4…'}    {'GGC*AC'}    {'> IL_51454.3  8…'}    {'AGAUAC*AU'}    {'> IL_51454.3  1…'}    {'CCCGAG*AG'}

  Columns 55 through 60

    {'> IL_51454.3  5…'}    {'AAU*CU'}    {'> IL_51454.3  7…'}    {'GAU*CC'}    {'> IL_51454.3  9…'}    {'CACGAU*AG'}

  Columns 61 through 66

    {'> IL_51454.3  7…'}    {'GAU*CC'}    {'> IL_51454.3  4…'}    {'GAU*CC'}    {'> IL_51454.3  9…'}    {'GAU*CC'}

  Columns 67 through 72

    {'> IL_51454.3  8…'}    {'AGAUAC*AU'}    {'> IL_51454.3  9…'}    {'GAU*CC'}    {'> IL_51454.3  4…'}    {'GGGCAC*AC'}

  Columns 73 through 78

    {'> IL_51454.3  4…'}    {'UGU*UA'}    {'> IL_51454.3  4…'}    {'GAU*CC'}    {'> IL_51454.3  8…'}    {'GAU*CC'}

  Columns 79 through 84

    {'> IL_51454.3  3…'}    {'ACG*AU'}    {'> IL_51454.3  4…'}    {'AGAUAC*AU'}    {'> IL_51454.3  3…'}    {'AGAUCC*CU'}

  Columns 85 through 90

    {'> IL_51454.3  5…'}    {'AGAUAC*AU'}    {'> IL_51454.3  8…'}    {'UAU*AA'}    {'> IL_51454.3  8…'}    {'GGC*AC'}

pCalculateTransitions:  processing IL_51479.1
  Columns 1 through 6

    {'> IL_51479.1  2…'}    {'CGCU*AAAAG'}    {'> IL_51479.1  2…'}    {'CGCU*AAAAG'}    {'> IL_51479.1  2…'}    {'CGCU*AAAAG'}

  Columns 7 through 12

    {'> IL_51479.1  2…'}    {'CGCU*AAAAG'}    {'> IL_51479.1  3…'}    {'CGCC*GCCUG'}    {'> IL_51479.1  4…'}    {'CUUG*CUUG'}

  Columns 13 through 18

    {'> IL_51479.1  4…'}    {'GUGA*UGCC'}    {'> IL_51479.1  8…'}    {'AGAG*CCGU'}    {'> IL_51479.1  4…'}    {'CUUG*CUUG'}

  Columns 19 through 20

    {'> IL_51479.1  8…'}    {'AAUG*CAUU'}

pCalculateTransitions:  processing IL_52743.1
    {'> IL_52743.1  5NWQ U   18 A   35'}    {'UACGACA*AGA'}

pCalculateTransitions:  processing IL_53448.1
  Columns 1 through 6

    {'> IL_53448.1  5…'}    {'CUAAG*UAUG'}    {'> IL_53448.1  5…'}    {'CUAAG*UAUG'}    {'> IL_53448.1  6…'}    {'CUAAG*UAUG'}

  Columns 7 through 12

    {'> IL_53448.1  4…'}    {'CUAAG*UAUG'}    {'> IL_53448.1  1…'}    {'CUAAG*UAUG'}    {'> IL_53448.1  5…'}    {'CUAAG*UAUG'}

  Columns 13 through 18

    {'> IL_53448.1  6…'}    {'CUAAG*UAUG'}    {'> IL_53448.1  6…'}    {'CUAAG*UAUG'}    {'> IL_53448.1  2…'}    {'CUAAG*UAUG'}

  Columns 19 through 22

    {'> IL_53448.1  1…'}    {'CUACG*UAUG'}    {'> IL_53448.1  5…'}    {'CUAAG*UAUG'}

pCalculateTransitions:  processing IL_53581.1
    {'> IL_53581.1  6SY6 G    5…'}    {'GAGAAUGUUAUGG*CAGAGAAAAC'}    {'> IL_53581.1  6SY4 G    6…'}    {'GAGAAUGUUAUGG*CAGAGAAAAC'}

pCalculateTransitions:  processing IL_53596.1
    {'> IL_53596.1  6PMO G  159…'}    {'GUGGAACCG*UC'}    {'> IL_53596.1  6UFH G  125…'}    {'GUGGCACCG*UC'}

pCalculateTransitions:  processing IL_53787.1
    {'> IL_53787.1  3IGI U  168 G  209'}    {'UGCUUUCUGCCA*AG'}

pCalculateTransitions:  processing IL_54041.2
  Columns 1 through 6

    {'> IL_54041.2  5…'}    {'GAAACG*AGAUAGC'}    {'> IL_54041.2  9…'}    {'GAAACG*AGAUAGC'}    {'> IL_54041.2  4…'}    {'GAAACG*AGAUAGC'}

  Columns 7 through 12

    {'> IL_54041.2  7…'}    {'GAAACG*AGAUAGC'}    {'> IL_54041.2  8…'}    {'GAAAGC*UAGUAGC'}    {'> IL_54041.2  8…'}    {'GAAAGC*UAGUAGC'}

  Columns 13 through 14

    {'> IL_54041.2  4…'}    {'GAAUCG*CAACAGC'}

pCalculateTransitions:  processing IL_54050.1
    {'> IL_54050.1  4KR6 U    8 G   28'}    {'UAGUGUCCUUG*CAAG'}

pCalculateTransitions:  processing IL_54177.4
  Columns 1 through 5

    {'> IL_54177.4  8…'}    {'GUGCCAG*CGGUAAUUC'}    {'> IL_54177.4  8…'}    {'GUGCCAG*CGGUAAUUC'}    {'> IL_54177.4  5…'}

  Columns 6 through 8

    {'GUGCCAG*CGGUAAUAC'}    {'> IL_54177.4  4…'}    {'GUGCCAG*CGGUAAUAC'}

pCalculateTransitions:  processing IL_54737.1
    {'> IL_54737.1  5J7L C 2103 G 2186'}    {'CCUUGAUGUGUAGGAUAG*CCUUUAAUG'}

pCalculateTransitions:  processing IL_54896.1
    {'> IL_54896.1  4XWF U   11 G   35'}    {'UGGCGAACAG*CGG'}

pCalculateTransitions:  processing IL_55516.2
  Columns 1 through 6

    {'> IL_55516.2  6…'}    {'CACG*AAG'}    {'> IL_55516.2  4…'}    {'UACAUGGGG*GGG'}    {'> IL_55516.2  7…'}    {'GACG*CAC'}

  Columns 7 through 11

    {'> IL_55516.2  8…'}    {'UACAUGGCG*CGG'}    {'> IL_55516.2  8…'}    {'UACAUGGCG*CGG'}    {'> IL_55516.2  3…'}

  Columns 12 through 14

    {'UACAUAACAAG*AACAA'}    {'> IL_55516.2  2…'}    {'UGCG*UAAA'}

pCalculateTransitions:  processing IL_55917.1
    {'> IL_55917.1  4KR9 U    8 G   28'}    {'UAGUGUCCU*AG'}

pCalculateTransitions:  processing IL_55953.3
  Columns 1 through 6

    {'> IL_55953.3  4…'}    {'GGACCC*GCUAAC'}    {'> IL_55953.3  4…'}    {'GGACCC*GCUAAC'}    {'> IL_55953.3  6…'}    {'GGAACC*GCUAAC'}

  Columns 7 through 8

    {'> IL_55953.3  4…'}    {'GGACCC*GCUAAC'}

pCalculateTransitions:  processing IL_56317.1
    {'> IL_56317.1  8CRE U 1623…'}    {'UCUUCG*GAAUA'}    {'> IL_56317.1  8P9A U 1627…'}    {'UCUUCG*GAAUA'}

pCalculateTransitions:  processing IL_56455.6
  Columns 1 through 5

    {'> IL_56455.6  1…'}    {'CGAGAGUAG*CGAUG…'}    {'> IL_56455.6  3…'}    {'CGAGAGUAG*CGAUG…'}    {'> IL_56455.6  5…'}

  Columns 6 through 10

    {'CGAGAGUAG*CGAUG…'}    {'> IL_56455.6  1…'}    {'CGAGAGUAG*CGAUG…'}    {'> IL_56455.6  9…'}    {'GGAGAGUAG*CGAUG…'}

  Columns 11 through 14

    {'> IL_56455.6  7…'}    {'GAAAAGUCG*CAAUG…'}    {'> IL_56455.6  3…'}    {'CGAGAGUAG*CGAUG…'}

pCalculateTransitions:  processing IL_56987.1
    {'> IL_56987.1  5…'}    {'UCG*UA'}    {'> IL_56987.1  6…'}    {'CGCGUUC*UG'}    {'> IL_56987.1  5…'}    {'GCG*AC'}

pCalculateTransitions:  processing IL_57188.5
  Columns 1 through 6

    {'> IL_57188.5  9…'}    {'CUAAGUG*CUUAAG'}    {'> IL_57188.5  4…'}    {'UUAAGUG*CUCAAA'}    {'> IL_57188.5  5…'}    {'UUAAGUG*CUAAA'}

  Columns 7 through 10

    {'> IL_57188.5  4…'}    {'UUAAGUG*CUAAA'}    {'> IL_57188.5  7…'}    {'CUCAGUG*CUCAAG'}

pCalculateTransitions:  processing IL_57741.1
    {'> IL_57741.1  8P9A U  893 A  919'}    {'UUGUCAGCU*UGGAUUUA'}

pCalculateTransitions:  processing IL_57744.1
  Columns 1 through 6

    {'> IL_57744.1  5…'}    {'GAAG*CAC'}    {'> IL_57744.1  3…'}    {'GAAG*CGC'}    {'> IL_57744.1  3…'}    {'GAAG*CGC'}

  Columns 7 through 12

    {'> IL_57744.1  8…'}    {'GUUU*GAC'}    {'> IL_57744.1  6…'}    {'GGA*UAC'}    {'> IL_57744.1  7…'}    {'UAU*AAA'}

  Columns 13 through 18

    {'> IL_57744.1  4…'}    {'GAGC*GAC'}    {'> IL_57744.1  1…'}    {'GCCG*CAC'}    {'> IL_57744.1  5…'}    {'CAG*UAG'}

  Columns 19 through 24

    {'> IL_57744.1  2…'}    {'GAAG*CAC'}    {'> IL_57744.1  7…'}    {'CGAC*GAG'}    {'> IL_57744.1  6…'}    {'CAGC*GGG'}

  Columns 25 through 30

    {'> IL_57744.1  4…'}    {'AAAG*CGU'}    {'> IL_57744.1  5…'}    {'GAAA*UGC'}    {'> IL_57744.1  4…'}    {'AAAG*CGU'}

  Columns 31 through 36

    {'> IL_57744.1  7…'}    {'CAGU*GGG'}    {'> IL_57744.1  9…'}    {'GAUG*CGC'}    {'> IL_57744.1  5…'}    {'GAUG*CGC'}

  Columns 37 through 42

    {'> IL_57744.1  4…'}    {'GAUG*CGC'}    {'> IL_57744.1  7…'}    {'GAUG*CGC'}    {'> IL_57744.1  5…'}    {'CCG*UAG'}

  Columns 43 through 44

    {'> IL_57744.1  7…'}    {'CAGC*GGG'}

pCalculateTransitions:  processing IL_57881.1
    {'> IL_57881.1  4V9F G  868 C  884'}    {'GGGC*UC'}

pCalculateTransitions:  processing IL_58103.11
  Columns 1 through 6

    {'> IL_58103.11  …'}    {'UACCC*GAACA'}    {'> IL_58103.11  …'}    {'ACCCC*GAACU'}    {'> IL_58103.11  …'}    {'UUCCC*GAACA'}

  Columns 7 through 12

    {'> IL_58103.11  …'}    {'UCCCC*GAUCA'}    {'> IL_58103.11  …'}    {'UUCCC*GAUCA'}    {'> IL_58103.11  …'}    {'UUCCC*GAACA'}

  Columns 13 through 18

    {'> IL_58103.11  …'}    {'ACCCC*GAACU'}    {'> IL_58103.11  …'}    {'ACCCC*GAACU'}    {'> IL_58103.11  …'}    {'ACCCC*GAACU'}

pCalculateTransitions:  processing IL_58112.2
  Columns 1 through 6

    {'> IL_58112.2  4…'}    {'GGGC*GGUAC'}    {'> IL_58112.2  5…'}    {'GAAG*CCUGC'}    {'> IL_58112.2  6…'}    {'GGAC*GAAAC'}

  Columns 7 through 8

    {'> IL_58112.2  6…'}    {'UUUCC*GACAA'}

pCalculateTransitions:  processing IL_58126.1
    {'> IL_58126.1  6VMY C  326…'}    {'CACGAAUU*ACAGAUG'}    {'> IL_58126.1  8P9A G  517…'}    {'GGAUAAAUC*GGAAUAC'}

pCalculateTransitions:  processing IL_58350.1
    {'> IL_58350.1  2NZ4 U   96 G  126'}    {'UUAAAUCGG*ACAAAG'}

pCalculateTransitions:  processing IL_58960.1
    {'> IL_58960.1  4…'}    {'UAAAGAGUG*CA'}    {'> IL_58960.1  4…'}    {'UAAAGAGUG*CA'}    {'> IL_58960.1  4…'}    {'AAAAGCAUG*CU'}

pCalculateTransitions:  processing IL_59049.1
    {'> IL_59049.1  8P9A G  751…'}    {'GAAAAAAUU*AUAUUAGC'}    {'> IL_59049.1  8CRE G  736…'}    {'GAAAAAAUU*AUAUUAGC'}

pCalculateTransitions:  processing IL_59258.1
    {'> IL_59258.1  5XTM G    8 C   39'}    {'GAUGAAA*UAACC'}

pCalculateTransitions:  processing IL_59302.1
    {'> IL_59302.1  4V9F U  548…'}    {'UACAAG*CGA'}    {'> IL_59302.1  3LQX U  139…'}    {'UACCAG*CAA'}

pCalculateTransitions:  processing IL_59724.1
    {'> IL_59724.1  4V9F C  290 G  362'}    {'CCGACCGC*CAGUACG'}

pCalculateTransitions:  processing IL_59877.1
    {'> IL_59877.1  1XJR G   19…'}    {'GCG*AUC'}    {'> IL_59877.1  5Y58 U  308…'}    {'UGUAUAU*AUA'}

pCalculateTransitions:  processing IL_60448.1
    {'> IL_60448.1  3NPQ G    7 C   32'}    {'GGAGCGCUGCAAG*CCCAGGC'}

pCalculateTransitions:  processing IL_60657.1
    {'> IL_60657.1  4ZNP C   12 G   37'}    {'CUGGCGGAUUAG*CGUG'}

pCalculateTransitions:  processing IL_60797.1
  Columns 1 through 5

    {'> IL_60797.1  2…'}    {'GAGAAACAC*GGUAC…'}    {'> IL_60797.1  3…'}    {'GAGAAACAC*GGUCC…'}    {'> IL_60797.1  3…'}

  Columns 6 through 8

    {'GAGAAACAC*GGUAC…'}    {'> IL_60797.1  1…'}    {'GAGAAACAC*GGUAU…'}

pCalculateTransitions:  processing IL_61242.1
    {'> IL_61242.1  4Z31 C    6 G   10'}    {'CUGUG*CUGUG'}

pCalculateTransitions:  processing IL_61249.1
    {'> IL_61249.1  5J7L U 1851 G 1891'}    {'UUAAUUGAUG*UUGAUCGAAG'}

pCalculateTransitions:  processing IL_61258.15
  Columns 1 through 6

    {'> IL_61258.15  …'}    {'CCA*UG'}    {'> IL_61258.15  …'}    {'CCA*UG'}    {'> IL_61258.15  …'}    {'UCA*UA'}

  Columns 7 through 12

    {'> IL_61258.15  …'}    {'CCA*UG'}    {'> IL_61258.15  …'}    {'ACU*AU'}    {'> IL_61258.15  …'}    {'UCG*CA'}

  Columns 13 through 18

    {'> IL_61258.15  …'}    {'GCG*CC'}    {'> IL_61258.15  …'}    {'GCU*AC'}    {'> IL_61258.15  …'}    {'GCG*CC'}

  Columns 19 through 24

    {'> IL_61258.15  …'}    {'UCG*CA'}    {'> IL_61258.15  …'}    {'UCU*AA'}    {'> IL_61258.15  …'}    {'GCU*AC'}

  Columns 25 through 30

    {'> IL_61258.15  …'}    {'GCG*CC'}    {'> IL_61258.15  …'}    {'GCU*AC'}    {'> IL_61258.15  …'}    {'UCG*CA'}

  Columns 31 through 36

    {'> IL_61258.15  …'}    {'GCU*AC'}    {'> IL_61258.15  …'}    {'GCG*CC'}    {'> IL_61258.15  …'}    {'GCU*AC'}

  Columns 37 through 42

    {'> IL_61258.15  …'}    {'ACU*AU'}    {'> IL_61258.15  …'}    {'GCU*AC'}    {'> IL_61258.15  …'}    {'UCG*CA'}

  Columns 43 through 48

    {'> IL_61258.15  …'}    {'ACU*AU'}    {'> IL_61258.15  …'}    {'UCG*CA'}    {'> IL_61258.15  …'}    {'GCG*CC'}

  Columns 49 through 54

    {'> IL_61258.15  …'}    {'UCA*UA'}    {'> IL_61258.15  …'}    {'GCC*GC'}    {'> IL_61258.15  …'}    {'GCG*CC'}

  Columns 55 through 60

    {'> IL_61258.15  …'}    {'GCG*CC'}    {'> IL_61258.15  …'}    {'GCU*AC'}    {'> IL_61258.15  …'}    {'UCG*CA'}

  Columns 61 through 66

    {'> IL_61258.15  …'}    {'UCA*UA'}    {'> IL_61258.15  …'}    {'GCG*CC'}    {'> IL_61258.15  …'}    {'GCG*CC'}

  Columns 67 through 72

    {'> IL_61258.15  …'}    {'GCG*CC'}    {'> IL_61258.15  …'}    {'GCG*CC'}    {'> IL_61258.15  …'}    {'UCA*UA'}

  Columns 73 through 78

    {'> IL_61258.15  …'}    {'CCG*CG'}    {'> IL_61258.15  …'}    {'CCC*GG'}    {'> IL_61258.15  …'}    {'GCC*GC'}

  Columns 79 through 82

    {'> IL_61258.15  …'}    {'GCG*CC'}    {'> IL_61258.15  …'}    {'UCC*GG'}

pCalculateTransitions:  processing IL_61286.1
    {'> IL_61286.1  3IGI C  296 G  321'}    {'CAUAGUAC*GGAAGG'}

pCalculateTransitions:  processing IL_61299.4
    {'> IL_61299.4  8…'}    {'UCUAAG*CUG'}    {'> IL_61299.4  8…'}    {'UCUAAG*CUG'}    {'> IL_61299.4  5…'}    {'CGGAAA*UGG'}

pCalculateTransitions:  processing IL_61341.1
    {'> IL_61341.1  3OXE C   31…'}    {'CGAAG*CAG'}    {'> IL_61341.1  8CRE U 1036…'}    {'UUGU*ACG'}

pCalculateTransitions:  processing IL_61438.4
  Columns 1 through 6

    {'> IL_61438.4  8…'}    {'CCGC*AAG'}    {'> IL_61438.4  8…'}    {'CCGC*AAG'}    {'> IL_61438.4  5…'}    {'CCGC*AAG'}

  Columns 7 through 8

    {'> IL_61438.4  4…'}    {'CCGC*AAG'}

pCalculateTransitions:  processing IL_61440.1
    {'> IL_61440.1  4UYK C   86 G  115'}    {'CGAAG*UGGAG'}

pCalculateTransitions:  processing IL_61476.2
  Columns 1 through 6

    {'> IL_61476.2  4…'}    {'CAGCG*AAG'}    {'> IL_61476.2  9…'}    {'CAGCG*GAG'}    {'> IL_61476.2  4…'}    {'CAGCA*UAG'}

  Columns 7 through 12

    {'> IL_61476.2  8…'}    {'CAUAG*UAG'}    {'> IL_61476.2  8…'}    {'CAUAG*UAG'}    {'> IL_61476.2  7…'}    {'CAAUG*UAG'}

  Columns 13 through 14

    {'> IL_61476.2  5…'}    {'AAUAG*GUU'}

pCalculateTransitions:  processing IL_62012.1
    {'> IL_62012.1  2O3Y C    7 G   42'}    {'CGCUA*AAAG'}

pCalculateTransitions:  processing IL_62654.1
    {'> IL_62654.1  4V9F C 1570 G 1627'}    {'CGAAC*GCAUAG'}

pCalculateTransitions:  processing IL_63519.1
    {'> IL_63519.1  8D28 G    4…'}    {'GAUAC*GCAGC'}    {'> IL_63519.1  8DK7 G    4…'}    {'GAUAC*GCAGC'}

pCalculateTransitions:  processing IL_63596.11
  Columns 1 through 6

    {'> IL_63596.11  …'}    {'UCACU*AAA'}    {'> IL_63596.11  …'}    {'CCGCU*AUG'}    {'> IL_63596.11  …'}    {'CCUCU*AUG'}

  Columns 7 through 12

    {'> IL_63596.11  …'}    {'CCUCU*AUG'}    {'> IL_63596.11  …'}    {'CCACU*AUG'}    {'> IL_63596.11  …'}    {'GCUCU*AUC'}

  Columns 13 through 18

    {'> IL_63596.11  …'}    {'GCUCC*GUC'}    {'> IL_63596.11  …'}    {'CCACU*ACG'}    {'> IL_63596.11  …'}    {'CCUCU*ACG'}

  Columns 19 through 24

    {'> IL_63596.11  …'}    {'UCCCU*ACCA'}    {'> IL_63596.11  …'}    {'GCACU*AGC'}    {'> IL_63596.11  …'}    {'CCUCU*ACG'}

  Columns 25 through 30

    {'> IL_63596.11  …'}    {'UCCCU*ACCA'}    {'> IL_63596.11  …'}    {'CCUCU*ACG'}    {'> IL_63596.11  …'}    {'GCUCU*AUC'}

  Columns 31 through 36

    {'> IL_63596.11  …'}    {'CCAAC*GGG'}    {'> IL_63596.11  …'}    {'GCAAU*AGC'}    {'> IL_63596.11  …'}    {'UCAAC*GGA'}

  Columns 37 through 38

    {'> IL_63596.11  …'}    {'UCAAC*GGA'}

pCalculateTransitions:  processing IL_63775.1
    {'> IL_63775.1  5O6U C    3 G   25'}    {'CCG*CG'}

pCalculateTransitions:  processing IL_64048.1
    {'> IL_64048.1  4MGN C   37…'}    {'CCGAAGCGAG*UG'}    {'> IL_64048.1  4JRC C   37…'}    {'CCGAAGCGAG*UG'}

pCalculateTransitions:  processing IL_64231.5
  Columns 1 through 6

    {'> IL_64231.5  4…'}    {'CUACC*GAUG'}    {'> IL_64231.5  5…'}    {'CUGCC*GAUG'}    {'> IL_64231.5  3…'}    {'GCAAG*CACC'}

  Columns 7 through 12

    {'> IL_64231.5  3…'}    {'GCAAG*CACC'}    {'> IL_64231.5  3…'}    {'GUAAC*GCCC'}    {'> IL_64231.5  2…'}    {'AAAAG*CGCU'}

  Columns 13 through 18

    {'> IL_64231.5  5…'}    {'CUAAC*GGUG'}    {'> IL_64231.5  8…'}    {'CCCAC*GUUG'}    {'> IL_64231.5  1…'}    {'UUUCU*GAAA'}

  Columns 19 through 22

    {'> IL_64231.5  1…'}    {'CAAGC*GAAG'}    {'> IL_64231.5  8…'}    {'AAAAG*CGCU'}

pCalculateTransitions:  processing IL_64403.1
    {'> IL_64403.1  5U30 U   28 G   58'}    {'UGUGCCAAUGG*CAAAG'}

pCalculateTransitions:  processing IL_64842.1
    {'> IL_64842.1  5ML7 C 2170 G 2204'}    {'CACUACAC*GAG'}

pCalculateTransitions:  processing IL_64858.3
  Columns 1 through 5

    {'> IL_64858.3  8…'}    {'GACGGUCGGGUAG*U…'}    {'> IL_64858.3  8…'}    {'GACGGUCGGGUGGGC…'}    {'> IL_64858.3  8…'}

  Columns 6 through 10

    {'GACGGUCGGGUAG*U…'}    {'> IL_64858.3  4…'}    {'GAAGGACGGGUAG*U…'}    {'> IL_64858.3  7…'}    {'GAGGGUCGGGUAG*U…'}

  Columns 11 through 12

    {'> IL_64858.3  4…'}    {'GAAGGACGGGUAG*U…'}

pCalculateTransitions:  processing IL_64900.1
  Columns 1 through 5

    {'> IL_64900.1  6…'}    {'CCGAUGAAU*AUGAAG'}    {'> IL_64900.1  6…'}    {'CCGAUGAAU*AUGAAG'}    {'> IL_64900.1  6…'}

  Column 6

    {'CCGAUGAAU*AUGAAG'}

pCalculateTransitions:  processing IL_65594.1
    {'> IL_65594.1  8P9A C   82…'}    {'CUUAGUAA*UGAAGCG'}    {'> IL_65594.1  8CRE C   81…'}    {'CUCAGUAG*UGAAGCG'}

pCalculateTransitions:  processing IL_65653.1
  Columns 1 through 5

    {'> IL_65653.1  8…'}    {'GAUUGUAAACAG*CG…'}    {'> IL_65653.1  8…'}    {'GAUUGUAAACAU*AG…'}    {'> IL_65653.1  8…'}

  Columns 6 through 8

    {'GAUUGUAAACAU*AG…'}    {'> IL_65653.1  8…'}    {'GAUUGUAAACAG*CG…'}

pCalculateTransitions:  processing IL_65718.4
  Columns 1 through 6

    {'> IL_65718.4  8…'}    {'GCCCG*UAAC'}    {'> IL_65718.4  8…'}    {'GCCCG*UAAC'}    {'> IL_65718.4  5…'}    {'GCCCG*UAAC'}

  Columns 7 through 8

    {'> IL_65718.4  4…'}    {'GCCCG*UAAC'}

pCalculateTransitions:  processing IL_65851.3
    {'> IL_65851.3  3KTW G  201…'}    {'GCCAGGC*GAGCAAC'}    {'> IL_65851.3  3NDB G  200…'}    {'GCCAGGC*GAGCAAC'}

pCalculateTransitions:  processing IL_66635.5
  Columns 1 through 6

    {'> IL_66635.5  6…'}    {'AUCUG*CU'}    {'> IL_66635.5  6…'}    {'GGAC*GC'}    {'> IL_66635.5  1…'}    {'AAUG*CU'}

  Columns 7 through 12

    {'> IL_66635.5  1…'}    {'GAUG*CC'}    {'> IL_66635.5  6…'}    {'CUGG*CG'}    {'> IL_66635.5  5…'}    {'AUUG*CU'}

  Columns 13 through 18

    {'> IL_66635.5  9…'}    {'UGAA*UG'}    {'> IL_66635.5  8…'}    {'GUCG*CC'}    {'> IL_66635.5  5…'}    {'GGUC*GC'}

  Columns 19 through 24

    {'> IL_66635.5  5…'}    {'GCUG*CC'}    {'> IL_66635.5  7…'}    {'UGC*GG'}    {'> IL_66635.5  3…'}    {'GGAA*UC'}

  Columns 25 through 30

    {'> IL_66635.5  8…'}    {'GUUG*CC'}    {'> IL_66635.5  5…'}    {'GGU*AC'}    {'> IL_66635.5  4…'}    {'GUUG*CC'}

  Columns 31 through 36

    {'> IL_66635.5  6…'}    {'UGC*GG'}    {'> IL_66635.5  7…'}    {'GUUG*CC'}    {'> IL_66635.5  5…'}    {'UAC*GG'}

  Columns 37 through 42

    {'> IL_66635.5  1…'}    {'GGC*GC'}    {'> IL_66635.5  8…'}    {'GUUG*CC'}    {'> IL_66635.5  4…'}    {'UAC*GG'}

  Columns 43 through 48

    {'> IL_66635.5  9…'}    {'CGC*GG'}    {'> IL_66635.5  7…'}    {'UGAA*UG'}    {'> IL_66635.5  7…'}    {'UGG*CG'}

  Columns 49 through 54

    {'> IL_66635.5  1…'}    {'CGC*GG'}    {'> IL_66635.5  7…'}    {'UGAU*AG'}    {'> IL_66635.5  3…'}    {'GUAC*GC'}

pCalculateTransitions:  processing IL_66663.1
    {'> IL_66663.1  8CRE U 1257 G 1424'}    {'UGCAUGGCG*UCUGUGAUG'}

pCalculateTransitions:  processing IL_66798.2
  Columns 1 through 6

    {'> IL_66798.2  9…'}    {'UUAAG*CGGAG'}    {'> IL_66798.2  5…'}    {'UUAAC*GGGAG'}    {'> IL_66798.2  7…'}    {'UUAAG*CGGAG'}

  Columns 7 through 12

    {'> IL_66798.2  4…'}    {'CUAAC*GGGAG'}    {'> IL_66798.2  4…'}    {'UUAAG*UGGAG'}    {'> IL_66798.2  4…'}    {'CGAAU*AGGAG'}

pCalculateTransitions:  processing IL_66997.2
    {'> IL_66997.2  4YAZ A    4…'}    {'ACACGA*AAU'}    {'> IL_66997.2  5J7L G  212…'}    {'GGCGGCCAGGG*ACC'}

pCalculateTransitions:  processing IL_67095.2
  Columns 1 through 6

    {'> IL_67095.2  4…'}    {'UAA*UCA'}    {'> IL_67095.2  8…'}    {'AAG*CCU'}    {'> IL_67095.2  7…'}    {'UAA*UCA'}

  Columns 7 through 12

    {'> IL_67095.2  5…'}    {'GAA*UCC'}    {'> IL_67095.2  8…'}    {'AAG*CCU'}    {'> IL_67095.2  9…'}    {'CAA*UCG'}

  Columns 13 through 16

    {'> IL_67095.2  4…'}    {'UAG*CCA'}    {'> IL_67095.2  9…'}    {'UAG*CAGG'}

pCalculateTransitions:  processing IL_67623.1
    {'> IL_67623.1  4V9F G   21 C   59'}    {'GGUUGCCU*AUAAGC'}

pCalculateTransitions:  processing IL_67767.4
  Columns 1 through 6

    {'> IL_67767.4  5…'}    {'CUAAG*UAUG'}    {'> IL_67767.4  4…'}    {'CUAAG*UAUG'}    {'> IL_67767.4  1…'}    {'CUAAG*UAUG'}

  Columns 7 through 12

    {'> IL_67767.4  5…'}    {'CUAAG*UAUG'}    {'> IL_67767.4  3…'}    {'CUAAG*UAUG'}    {'> IL_67767.4  5…'}    {'CUAAG*UAUG'}

  Columns 13 through 14

    {'> IL_67767.4  1…'}    {'CUAAG*UAUG'}

pCalculateTransitions:  processing IL_67780.1
    {'> IL_67780.1  4WF9 G 1476 C 1608'}    {'GUAGG*CACAC'}

pCalculateTransitions:  processing IL_68140.4
  Columns 1 through 6

    {'> IL_68140.4  1…'}    {'AAAC*GU'}    {'> IL_68140.4  1…'}    {'AAAC*GU'}    {'> IL_68140.4  5…'}    {'AUAC*GU'}

  Columns 7 through 12

    {'> IL_68140.4  4…'}    {'AUAU*AU'}    {'> IL_68140.4  4…'}    {'AUAC*GU'}    {'> IL_68140.4  1…'}    {'AUAC*GU'}

  Columns 13 through 18

    {'> IL_68140.4  8…'}    {'GAAU*AC'}    {'> IL_68140.4  8…'}    {'GAAU*AC'}    {'> IL_68140.4  9…'}    {'GAAG*CC'}

  Columns 19 through 24

    {'> IL_68140.4  4…'}    {'GAAG*CC'}    {'> IL_68140.4  4…'}    {'GAAG*CC'}    {'> IL_68140.4  5…'}    {'GAAG*CC'}

  Columns 25 through 30

    {'> IL_68140.4  5…'}    {'GAAG*CC'}    {'> IL_68140.4  7…'}    {'GAAG*CC'}    {'> IL_68140.4  4…'}    {'GAAG*CC'}

  Columns 31 through 36

    {'> IL_68140.4  4…'}    {'GUAU*AC'}    {'> IL_68140.4  1…'}    {'CAAG*CG'}    {'> IL_68140.4  1…'}    {'GAAAG*CC'}

pCalculateTransitions:  processing IL_68243.1
    {'> IL_68243.1  9DFE C  844 G  934'}    {'CGCUGAC*GGUGGAG'}

pCalculateTransitions:  processing IL_68405.1
    {'> IL_68405.1  2R8S C  121 G  200'}    {'CAACAGC*GACAUG'}

pCalculateTransitions:  processing IL_68574.4
    {'> IL_68574.4  5…'}    {'UAAG*UGAUG'}    {'> IL_68574.4  9…'}    {'UAAG*CGAUG'}    {'> IL_68574.4  3…'}    {'CACC*GCAAG'}

pCalculateTransitions:  processing IL_68909.1
  Columns 1 through 6

    {'> IL_68909.1  1…'}    {'CGCCG*GAGG'}    {'> IL_68909.1  8…'}    {'GGCUG*AUUC'}    {'> IL_68909.1  8…'}    {'GUUCUUGCUAUG*UAUC'}

  Columns 7 through 11

    {'> IL_68909.1  4…'}    {'GGGCG*GCCC'}    {'> IL_68909.1  8…'}    {'UAUAGAUAUGGUAC*…'}    {'> IL_68909.1  4…'}

  Column 12

    {'GGAACAAGGCACUAG…'}

pCalculateTransitions:  processing IL_69000.1
    {'> IL_69000.1  9C2K G    9…'}    {'GGGCGC*GAC'}    {'> IL_69000.1  9C2K G    9…'}    {'GGGCGC*GAC'}

pCalculateTransitions:  processing IL_69145.3
  Columns 1 through 6

    {'> IL_69145.3  5…'}    {'UCCUGC*GAAA'}    {'> IL_69145.3  4…'}    {'UCCUGC*GAAA'}    {'> IL_69145.3  4…'}    {'UCCAGC*GGAA'}

  Columns 7 through 8

    {'> IL_69145.3  3…'}    {'UCCUGC*GAAA'}

pCalculateTransitions:  processing IL_69229.3
  Columns 1 through 5

    {'> IL_69229.3  3…'}    {'CUGACGC*GUGAUG'}    {'> IL_69229.3  5…'}    {'CUGAAUU*GUGAUG'}    {'> IL_69229.3  5…'}

  Columns 6 through 10

    {'CUGAAAGUCGUAGUG…'}    {'> IL_69229.3  3…'}    {'CUGACGC*GUGAUG'}    {'> IL_69229.3  1…'}    {'CUGACGC*GUGAUG'}

  Columns 11 through 15

    {'> IL_69229.3  3…'}    {'UUGAGAGUUGUAGUA…'}    {'> IL_69229.3  6…'}    {'CCGAGCG*UUUGACG'}    {'> IL_69229.3  7…'}

  Column 16

    {'UGGAGCG*UGAAA'}

pCalculateTransitions:  processing IL_69271.3
    {'> IL_69271.3  5BTP C   15…'}    {'CUGACGGAACG*CAUG'}    {'> IL_69271.3  9BZC C   12…'}    {'CUGACGGAAG*CAUG'}

pCalculateTransitions:  processing IL_69440.3
    {'> IL_69440.3  5…'}    {'UAGCA*AAA'}    {'> IL_69440.3  9…'}    {'UAGCG*AAA'}    {'> IL_69440.3  4…'}    {'UAGCG*AAA'}

pCalculateTransitions:  processing IL_69543.3
  Columns 1 through 5

    {'> IL_69543.3  8…'}    {'CGGAAUU*GGAGAUG'}    {'> IL_69543.3  8…'}    {'UGGAAUU*GGAGAUG'}    {'> IL_69543.3  9…'}

  Column 6

    {'CAGAGAA*UGUGAGG'}

pCalculateTransitions:  processing IL_69986.1
    {'> IL_69986.1  3D0M U    7 A   12'}    {'UGAUGA*UGAUGA'}

pCalculateTransitions:  processing IL_70096.1
    {'> IL_70096.1  6MWN U  604 G  675'}    {'UUUG*CUUAUG'}

pCalculateTransitions:  processing IL_70335.1
    {'> IL_70335.1  9DFE A 2054…'}    {'ACGAU*CUAU'}    {'> IL_70335.1  7A0S A 2037…'}    {'ACGAU*CUAU'}

pCalculateTransitions:  processing IL_70376.1
    {'> IL_70376.1  8CRE U  168 A  253'}    {'UGUG*GUA'}

pCalculateTransitions:  processing IL_70411.2
  Columns 1 through 6

    {'> IL_70411.2  8…'}    {'UGUAAG*CUGAG'}    {'> IL_70411.2  8…'}    {'UGUAAG*CUGAG'}    {'> IL_70411.2  7…'}    {'UGCACG*UUCAG'}

  Columns 7 through 12

    {'> IL_70411.2  4…'}    {'UGUGCG*UUAAG'}    {'> IL_70411.2  4…'}    {'UGGAAG*UGGAG'}    {'> IL_70411.2  5…'}    {'UGUAAG*UUGAG'}

  Columns 13 through 14

    {'> IL_70411.2  9…'}    {'UGUAAG*UUGAG'}

pCalculateTransitions:  processing IL_70627.3
    {'> IL_70627.3  4…'}    {'GUGACGG*AGUC'}    {'> IL_70627.3  6…'}    {'GUAAUAG*AGCC'}    {'> IL_70627.3  4…'}    {'CUAAGCG*AAAUG'}

pCalculateTransitions:  processing IL_70670.1
    {'> IL_70670.1  4LCK G   15 C   91'}    {'GAAGAGUAU*AGAAGGCAC'}

pCalculateTransitions:  processing IL_70801.1
    {'> IL_70801.1  5J7L G  450 C  483'}    {'GAAGGGC*AUUGAC'}

pCalculateTransitions:  processing IL_70923.9
  Columns 1 through 6

    {'> IL_70923.9  5…'}    {'CGAAGAAC*GGGAG'}    {'> IL_70923.9  6…'}    {'CGAAGAAC*GGGAG'}    {'> IL_70923.9  5…'}    {'CGAAGAAC*GGGAG'}

  Columns 7 through 12

    {'> IL_70923.9  6…'}    {'CGAAGAAC*GGGAG'}    {'> IL_70923.9  5…'}    {'CUGCGAAG*UGGAG'}    {'> IL_70923.9  3…'}    {'CUGUGAAC*GGGAG'}

  Columns 13 through 18

    {'> IL_70923.9  6…'}    {'CGAAGAAC*GGGAG'}    {'> IL_70923.9  9…'}    {'CGAUGAAG*UGGAG'}    {'> IL_70923.9  7…'}    {'CGAAGAAC*GGGAG'}

  Columns 19 through 24

    {'> IL_70923.9  7…'}    {'CGAAGAAC*GGGAG'}    {'> IL_70923.9  5…'}    {'CGAAGAAC*GGGAG'}    {'> IL_70923.9  4…'}    {'GAUGGAAG*UGGAC'}

  Columns 25 through 30

    {'> IL_70923.9  7…'}    {'CUAUGAAG*UGGAG'}    {'> IL_70923.9  7…'}    {'CGAAGAAC*GGGAG'}    {'> IL_70923.9  3…'}    {'CGAUGAAA*UGGAG'}

  Columns 31 through 36

    {'> IL_70923.9  5…'}    {'AGACGAUC*GGGAU'}    {'> IL_70923.9  7…'}    {'CGAAGAAC*GGGAG'}    {'> IL_70923.9  7…'}    {'CUAUGAAG*UGGAG'}

  Columns 37 through 42

    {'> IL_70923.9  4…'}    {'CGAAGAAC*GGGAG'}    {'> IL_70923.9  7…'}    {'CGGAGAAG*UGGAG'}    {'> IL_70923.9  4…'}    {'CGUUGAAG*UGGAG'}

  Columns 43 through 48

    {'> IL_70923.9  7…'}    {'CGAAGAAC*GGGAG'}    {'> IL_70923.9  4…'}    {'CGACGAAG*CAGAG'}    {'> IL_70923.9  4…'}    {'UGAUGACC*GCAAG'}

  Columns 49 through 54

    {'> IL_70923.9  8…'}    {'UGACGAAG*UCGAA'}    {'> IL_70923.9  8…'}    {'UGACGAAG*UCGAA'}    {'> IL_70923.9  5…'}    {'CUUUGAAG*UGGAG'}

pCalculateTransitions:  processing IL_71294.3
    {'> IL_71294.3  1L9A C  190…'}    {'CCAGGU*GAGCAG'}    {'> IL_71294.3  4N0T A   95…'}    {'AGAGAC*GUCAAU'}

pCalculateTransitions:  processing IL_71598.1
    {'> IL_71598.1  6D3P U    6 A   36'}    {'UAACGG*AAA'}

pCalculateTransitions:  processing IL_73002.1
    {'> IL_73002.1  8P9A U  649 A  685'}    {'UUGGCCGUGGA*UUUCCAA'}

pCalculateTransitions:  processing IL_73355.1
    {'> IL_73355.1  8P9A G 1947…'}    {'GGCA*AC'}    {'> IL_73355.1  8CRE G 1943…'}    {'GGCA*AC'}

pCalculateTransitions:  processing IL_73452.2
    {'> IL_73452.2  8…'}    {'CUAG*CG'}    {'> IL_73452.2  1…'}    {'GUC*GC'}    {'> IL_73452.2  1…'}    {'GAAUG*CC'}

pCalculateTransitions:  processing IL_73700.1
    {'> IL_73700.1  6N5P C   36 G   99'}    {'CGCUUUUUGG*CGACAG'}

pCalculateTransitions:  processing IL_73759.1
    {'> IL_73759.1  7OAX G   10 C   44'}    {'GAGGGG*CGGUC'}

pCalculateTransitions:  processing IL_73789.1
    {'> IL_73789.1  8CRE G  361…'}    {'GGGCG*AUUC'}    {'> IL_73789.1  8P9A G  363…'}    {'GGGCG*AUUC'}

pCalculateTransitions:  processing IL_74051.1
    {'> IL_74051.1  5…'}    {'CGGUGAAG*CGAG'}    {'> IL_74051.1  5…'}    {'CGGUGAAG*CGAG'}    {'> IL_74051.1  5…'}    {'CGGUGAAG*CGAG'}

pCalculateTransitions:  processing IL_74184.1
    {'> IL_74184.1  4GXY C   95 G  130'}    {'CGGGAUGUG*CGG'}

pCalculateTransitions:  processing IL_74367.1
    {'> IL_74367.1  8P9A G  680…'}    {'GUUUG*CAUAC'}    {'> IL_74367.1  8CRE G  678…'}    {'GUUUG*CGUAC'}

pCalculateTransitions:  processing IL_74746.1
    {'> IL_74746.1  3HJW G    9…'}    {'GAAACCGCG*UUCGCUCC'}    {'> IL_74746.1  3HAX C    9…'}    {'CUUGAGUG*UAAUUAUG'}

pCalculateTransitions:  processing IL_74957.1
    {'> IL_74957.1  2R8S G  134 C  189'}    {'GUAUAA*AGC'}

pCalculateTransitions:  processing IL_75283.2
  Columns 1 through 5

    {'> IL_75283.2  3…'}    {'GGAGCGCCGGUGAA*…'}    {'> IL_75283.2  5…'}    {'GGAGCAACAGUGAA*…'}    {'> IL_75283.2  1…'}

  Column 6

    {'GGAGCGCCGGUGAA*…'}

pCalculateTransitions:  processing IL_75294.1
    {'> IL_75294.1  9DFE G 2843…'}    {'GGGGC*CGAC'}    {'> IL_75294.1  5WTI C   25…'}    {'CAACAACGGAGCG*CGAGG'}

pCalculateTransitions:  processing IL_76308.6
  Columns 1 through 6

    {'> IL_76308.6  1…'}    {'UCAGGU*AAGCAG'}    {'> IL_76308.6  1…'}    {'CCAGGU*GAGCAG'}    {'> IL_76308.6  3…'}    {'UCAGGU*AAGCAG'}

  Columns 7 through 10

    {'> IL_76308.6  6…'}    {'CUACCC*GAACAG'}    {'> IL_76308.6  8…'}    {'GGCCAG*CUCAAC'}

pCalculateTransitions:  processing IL_76319.5
    {'> IL_76319.5  8…'}    {'UGCAU*AUG'}    {'> IL_76319.5  4…'}    {'UGCAU*AUG'}    {'> IL_76319.5  8…'}    {'UGCAU*AUG'}

pCalculateTransitions:  processing IL_76460.1
    {'> IL_76460.1  6R47 C   28 G   63'}    {'CUCAGACCCGAAGCGUG*CGGUG'}

pCalculateTransitions:  processing IL_76709.2
  Columns 1 through 6

    {'> IL_76709.2  1…'}    {'CCGA*AG'}    {'> IL_76709.2  8…'}    {'GCGA*CC'}    {'> IL_76709.2  1…'}    {'GGGCUAUA*UC'}

  Columns 7 through 8

    {'> IL_76709.2  4…'}    {'GUAA*UC'}

pCalculateTransitions:  processing IL_76758.2
  Columns 1 through 6

    {'> IL_76758.2  5…'}    {'ACUAGG*CUGU'}    {'> IL_76758.2  4…'}    {'ACUCGG*CUGU'}    {'> IL_76758.2  9…'}    {'ACUCUG*CUGU'}

  Columns 7 through 12

    {'> IL_76758.2  4…'}    {'AUUCGG*CUGU'}    {'> IL_76758.2  7…'}    {'ACUUUG*CUGU'}    {'> IL_76758.2  8…'}    {'AGUCGG*CUGU'}

  Columns 13 through 14

    {'> IL_76758.2  8…'}    {'AGUCGG*CUGU'}

pCalculateTransitions:  processing IL_77045.1
    {'> IL_77045.1  3IGI A  149 U  225'}    {'AUAUGAGG*UAAAU'}

pCalculateTransitions:  processing IL_77278.1
    {'> IL_77278.1  8CRE C 1183…'}    {'CUCAUCAG*CUCAAG'}    {'> IL_77278.1  8P9A C 1187…'}    {'CUCAUCAG*CUCAAG'}

pCalculateTransitions:  processing IL_77658.1
  Columns 1 through 6

    {'> IL_77658.1  8…'}    {'ACUG*CUUU'}    {'> IL_77658.1  8…'}    {'CUUG*CUUG'}    {'> IL_77658.1  3…'}    {'CUUG*CUUG'}

  Columns 7 through 12

    {'> IL_77658.1  8…'}    {'AUUG*CUUU'}    {'> IL_77658.1  6…'}    {'AUUG*CUUU'}    {'> IL_77658.1  8…'}    {'GCUG*CUCC'}

  Columns 13 through 18

    {'> IL_77658.1  4…'}    {'GUUC*GUUC'}    {'> IL_77658.1  8…'}    {'UUUG*CUUA'}    {'> IL_77658.1  2…'}    {'CUUG*CUUG'}

  Columns 19 through 24

    {'> IL_77658.1  8…'}    {'UUUG*CUUA'}    {'> IL_77658.1  4…'}    {'CUUG*CUUG'}    {'> IL_77658.1  7…'}    {'AUUC*GUCU'}

  Columns 25 through 30

    {'> IL_77658.1  5…'}    {'CUAG*CCUG'}    {'> IL_77658.1  8…'}    {'GUCG*CUUC'}    {'> IL_77658.1  3…'}    {'CUUC*GUCG'}

  Columns 31 through 36

    {'> IL_77658.1  6…'}    {'CUCC*GUUG'}    {'> IL_77658.1  8…'}    {'CUCA*UUUG'}    {'> IL_77658.1  2…'}    {'CUUC*GUCG'}

  Columns 37 through 42

    {'> IL_77658.1  8…'}    {'CUCC*GUUG'}    {'> IL_77658.1  8…'}    {'UUCU*AUUA'}    {'> IL_77658.1  8…'}    {'UUUC*GUUA'}

  Columns 43 through 48

    {'> IL_77658.1  8…'}    {'CUUA*UUUG'}    {'> IL_77658.1  8…'}    {'UUUC*GUUA'}    {'> IL_77658.1  8…'}    {'UUCU*AUUA'}

  Columns 49 through 54

    {'> IL_77658.1  2…'}    {'UUUG*UUUG'}    {'> IL_77658.1  4…'}    {'CCUG*CCUG'}    {'> IL_77658.1  8…'}    {'UUCC*GUUG'}

  Columns 55 through 60

    {'> IL_77658.1  8…'}    {'CUUG*CUUG'}    {'> IL_77658.1  4…'}    {'CCUG*CCUG'}    {'> IL_77658.1  4…'}    {'CCAG*CCAG'}

  Columns 61 through 66

    {'> IL_77658.1  7…'}    {'AGUUC*GUCU'}    {'> IL_77658.1  4…'}    {'CCUG*CCUG'}    {'> IL_77658.1  8…'}    {'CUUG*CUUG'}

  Columns 67 through 68

    {'> IL_77658.1  4…'}    {'CCUG*CCUG'}

pCalculateTransitions:  processing IL_77691.5
  Columns 1 through 6

    {'> IL_77691.5  5…'}    {'UUAGC*GAAG'}    {'> IL_77691.5  4…'}    {'UUAGC*GAAG'}    {'> IL_77691.5  3…'}    {'UGAGC*GGAA'}

  Columns 7 through 11

    {'> IL_77691.5  4…'}    {'CGAGAGCGAAGC*GAAG'}    {'> IL_77691.5  2…'}    {'UAACAAUGAAAG*AAAG'}    {'> IL_77691.5  3…'}

  Columns 12 through 14

    {'UGAGC*GGAA'}    {'> IL_77691.5  3…'}    {'UGAGC*AAAG'}

pCalculateTransitions:  processing IL_77870.1
    {'> IL_77870.1  4V9F C  280…'}    {'CUCUCAUC*GUGCG'}    {'> IL_77870.1  5J7L C  274…'}    {'CCUGAAUC*GUGAG'}

pCalculateTransitions:  processing IL_78349.3
    {'> IL_78349.3  4LFB U  605…'}    {'UGAAAGAC*GGGGAG'}    {'> IL_78349.3  5J7L U  605…'}    {'UGAAAUCC*GAACUG'}

pCalculateTransitions:  processing IL_78472.1
    {'> IL_78472.1  5UNE G   31 C   14'}    {'GGCGGAAA*UGGGC'}

pCalculateTransitions:  processing IL_78800.1
    {'> IL_78800.1  8CRE A 1330…'}    {'AAUAUU*CU'}    {'> IL_78800.1  8P9A A 1345…'}    {'AAUAUU*CU'}

pCalculateTransitions:  processing IL_79846.1
    {'> IL_79846.1  3Q3Z G   12 C   75'}    {'GAAUAGUAGUGCAACC*GAC'}

pCalculateTransitions:  processing IL_79895.1
    {'> IL_79895.1  8CRE G 2742…'}    {'GUCC*GC'}    {'> IL_79895.1  4LCK G   28…'}    {'GAUU*AC'}

pCalculateTransitions:  processing IL_80209.1
    {'> IL_80209.1  4LCK U   37 A   71'}    {'UGAUUAGCGAC*GGA'}

pCalculateTransitions:  processing IL_80231.1
    {'> IL_80231.1  5XTM G    8…'}    {'GAUGAAA*UAACC'}    {'> IL_80231.1  5J7L A 1430…'}    {'AAGAAG*CCACU'}

pCalculateTransitions:  processing IL_80298.1
    {'> IL_80298.1  4WT8 A    7 U   46'}    {'AUAGCAGGGGAUUGAAAAUUCCGA*GU'}

pCalculateTransitions:  processing IL_80398.1
    {'> IL_80398.1  4TS2 G   14 C   85'}    {'GAAA*UAAC'}

pCalculateTransitions:  processing IL_80412.1
    {'> IL_80412.1  6P2H U   22 A   52'}    {'UAAUAGCCU*CCA'}

pCalculateTransitions:  processing IL_80604.6
  Columns 1 through 5

    {'> IL_80604.6  8…'}    {'GUAUAAC*GCUAAUAC'}    {'> IL_80604.6  8…'}    {'GGAUAAC*GCUAAUAC'}    {'> IL_80604.6  5…'}

  Column 6

    {'GGAUAAC*GCUAAUAC'}

pCalculateTransitions:  processing IL_80926.1
  Columns 1 through 6

    {'> IL_80926.1  3…'}    {'CAGUCCG*AGAAG'}    {'> IL_80926.1  3…'}    {'CAGUCCG*AGAAG'}    {'> IL_80926.1  1…'}    {'CAGUCCG*AGAAG'}

  Columns 7 through 12

    {'> IL_80926.1  3…'}    {'CAGUCCG*AGAAG'}    {'> IL_80926.1  2…'}    {'CUGUCCG*AGAAG'}    {'> IL_80926.1  1…'}    {'CAGUCCG*AGAAG'}

  Columns 13 through 14

    {'> IL_80926.1  1…'}    {'CAGUCCG*AGAAG'}

pCalculateTransitions:  processing IL_81392.1
    {'> IL_81392.1  6LT7 C   28 G   61'}    {'CUACACACUGCCCCU*UUCCG'}

pCalculateTransitions:  processing IL_81516.2
  Columns 1 through 5

    {'> IL_81516.2  5…'}    {'GAACGAGUGAAA*AG…'}    {'> IL_81516.2  7…'}    {'GAACGAGUGAAA*AG…'}    {'> IL_81516.2  9…'}

  Columns 6 through 10

    {'GAACGAGUGAAA*AG…'}    {'> IL_81516.2  4…'}    {'GCACGAGUGAAA*AG…'}    {'> IL_81516.2  8…'}    {'GAACGAGUGAAA*AG…'}

  Columns 11 through 12

    {'> IL_81516.2  8…'}    {'GAACGAGUGAAA*AG…'}

pCalculateTransitions:  processing IL_81522.2
    {'> IL_81522.2  4…'}    {'GUUAC*GUUC'}    {'> IL_81522.2  4…'}    {'GUUAC*GUUC'}    {'> IL_81522.2  6…'}    {'UAGGC*GG'}

pCalculateTransitions:  processing IL_81731.1
    {'> IL_81731.1  4M6D G   12 C   48'}    {'GGCUAAAGAGUG*CAGAC'}

pCalculateTransitions:  processing IL_81831.1
    {'> IL_81831.1  4R4V U  719…'}    {'UAAG*CA'}    {'> IL_81831.1  3WBM G    2…'}    {'GUA*UC'}

pCalculateTransitions:  processing IL_82107.4
  Columns 1 through 6

    {'> IL_82107.4  5…'}    {'AC*GACU'}    {'> IL_82107.4  7…'}    {'AC*GACU'}    {'> IL_82107.4  3…'}    {'GG*UAGC'}

  Columns 7 through 12

    {'> IL_82107.4  3…'}    {'GG*UAGC'}    {'> IL_82107.4  4…'}    {'UG*UCAA'}    {'> IL_82107.4  5…'}    {'AC*GACU'}

  Columns 13 through 18

    {'> IL_82107.4  8…'}    {'CG*CUAG'}    {'> IL_82107.4  5…'}    {'UG*UAAA'}    {'> IL_82107.4  8…'}    {'UG*UAAA'}

  Columns 19 through 24

    {'> IL_82107.4  1…'}    {'GG*UUUC'}    {'> IL_82107.4  8…'}    {'UG*UAAA'}    {'> IL_82107.4  1…'}    {'GG*UUUC'}

  Columns 25 through 30

    {'> IL_82107.4  5…'}    {'AG*CAAU'}    {'> IL_82107.4  5…'}    {'AG*CAAU'}    {'> IL_82107.4  8…'}    {'AA*UCGU'}

  Columns 31 through 36

    {'> IL_82107.4  6…'}    {'AC*GUCU'}    {'> IL_82107.4  8…'}    {'AA*UCGU'}    {'> IL_82107.4  1…'}    {'UG*CAAA'}

  Columns 37 through 42

    {'> IL_82107.4  4…'}    {'UG*UAAA'}    {'> IL_82107.4  5…'}    {'UG*CGAA'}    {'> IL_82107.4  4…'}    {'CG*CGUG'}

  Columns 43 through 48

    {'> IL_82107.4  4…'}    {'CG*CAUG'}    {'> IL_82107.4  1…'}    {'UG*UAAA'}    {'> IL_82107.4  5…'}    {'AC*GAAU'}

  Columns 49 through 54

    {'> IL_82107.4  4…'}    {'GG*CAGC'}    {'> IL_82107.4  4…'}    {'CG*UAAG'}    {'> IL_82107.4  9…'}    {'ACU*AUU'}

  Columns 55 through 60

    {'> IL_82107.4  8…'}    {'GG*UUUC'}    {'> IL_82107.4  7…'}    {'GAA*UAGC'}    {'> IL_82107.4  7…'}    {'GAA*UAGC'}

pCalculateTransitions:  processing IL_82292.1
    {'> IL_82292.1  8…'}    {'CGCAAG*CGCAAG'}    {'> IL_82292.1  4…'}    {'CCUUGG*CCUUGG'}    {'> IL_82292.1  3…'}    {'UACAGA*UAGGUA'}

pCalculateTransitions:  processing IL_82426.6
  Columns 1 through 5

    {'> IL_82426.6  8…'}    {'CGGGUAGUAG*UGUGUG'}    {'> IL_82426.6  4…'}    {'CGGGUAGUAG*AGUGUG'}    {'> IL_82426.6  8…'}

  Columns 6 through 10

    {'CGGGUGGGCGUGUGU…'}    {'> IL_82426.6  7…'}    {'CGGGUAGUAG*AGUGUG'}    {'> IL_82426.6  8…'}    {'CGGGUAGUAG*AGUGUG'}

  Columns 11 through 12

    {'> IL_82426.6  4…'}    {'CGGGUAGUAG*AGUGUG'}

pCalculateTransitions:  processing IL_82683.2
  Columns 1 through 6

    {'> IL_82683.2  7…'}    {'AGAGCA*AGUU'}    {'> IL_82683.2  7…'}    {'AGAGCA*AGUU'}    {'> IL_82683.2  5…'}    {'AGAGCA*AGUU'}

  Columns 7 through 12

    {'> IL_82683.2  5…'}    {'AGAGCA*AGUU'}    {'> IL_82683.2  7…'}    {'AGAGCA*AGUU'}    {'> IL_82683.2  7…'}    {'AGAGCA*AGUU'}

  Columns 13 through 18

    {'> IL_82683.2  7…'}    {'AGAGCA*AGUU'}    {'> IL_82683.2  5…'}    {'AGAGCA*AGUU'}    {'> IL_82683.2  5…'}    {'AGAGCA*AGUU'}

  Columns 19 through 22

    {'> IL_82683.2  8…'}    {'AGAGCA*AGUU'}    {'> IL_82683.2  8…'}    {'AGAGCA*AGUU'}

pCalculateTransitions:  processing IL_82706.1
    {'> IL_82706.1  8P9A C 1034…'}    {'CGAU*UUUGG'}    {'> IL_82706.1  8CRE C 1019…'}    {'CGAU*UUUGG'}

pCalculateTransitions:  processing IL_82741.2
    {'> IL_82741.2  8…'}    {'CAACG*UUG'}    {'> IL_82741.2  8…'}    {'CAACG*UUG'}    {'> IL_82741.2  8…'}    {'CCCUU*AG'}

pCalculateTransitions:  processing IL_82968.1
    {'> IL_82968.1  7JRT C   11…'}    {'CGGAGGCAC*GG'}    {'> IL_82968.1  7JRT C   11…'}    {'CGGAGGCAC*GG'}

pCalculateTransitions:  processing IL_83149.1
    {'> IL_83149.1  8CRE G 1190…'}    {'GACACCACAAAAUG*AAAAUGGAUG…'}    {'> IL_83149.1  8P9A G 1194…'}    {'GACACCACAAAAUG*AAAAUGGAUG…'}

pCalculateTransitions:  processing IL_83150.2
  Columns 1 through 6

    {'> IL_83150.2  4…'}    {'GGAAG*CGC'}    {'> IL_83150.2  7…'}    {'GGAAG*CGC'}    {'> IL_83150.2  8…'}    {'UAAUU*ACCA'}

  Columns 7 through 8

    {'> IL_83150.2  8…'}    {'UAAUU*ACCA'}

pCalculateTransitions:  processing IL_83389.2
  Columns 1 through 6

    {'> IL_83389.2  4…'}    {'AAG*CUAU'}    {'> IL_83389.2  4…'}    {'ACG*CUAU'}    {'> IL_83389.2  5…'}    {'ACG*CUAU'}

  Columns 7 through 10

    {'> IL_83389.2  8…'}    {'GAA*UACC'}    {'> IL_83389.2  8…'}    {'GAA*UACC'}

pCalculateTransitions:  processing IL_84251.1
    {'> IL_84251.1  7EDT U    5…'}    {'UCCG*UCCG'}    {'> IL_84251.1  4R4V C  637…'}    {'CAAG*CGAAG'}

pCalculateTransitions:  processing IL_84409.1
    {'> IL_84409.1  1NBS C  184 G  226'}    {'CACAGUGACGAAGU*AGUGGAACGCG'}

pCalculateTransitions:  processing IL_84476.1
  Columns 1 through 6

    {'> IL_84476.1  8…'}    {'CC*GUUG'}    {'> IL_84476.1  8…'}    {'CC*GUUG'}    {'> IL_84476.1  8…'}    {'CG*CUAG'}

  Columns 7 through 12

    {'> IL_84476.1  7…'}    {'CC*GUUG'}    {'> IL_84476.1  7…'}    {'CG*CUAG'}    {'> IL_84476.1  7…'}    {'CC*GUUG'}

  Columns 13 through 18

    {'> IL_84476.1  7…'}    {'CUAG*CG'}    {'> IL_84476.1  1…'}    {'GUUCG*CC'}    {'> IL_84476.1  1…'}    {'GUUCG*CC'}

  Columns 19 through 24

    {'> IL_84476.1  3…'}    {'GCUC*GC'}    {'> IL_84476.1  6…'}    {'AC*GAUU'}    {'> IL_84476.1  6…'}    {'CU*AUUG'}

  Columns 25 through 26

    {'> IL_84476.1  4…'}    {'CGAC*GG'}

pCalculateTransitions:  processing IL_84665.1
    {'> IL_84665.1  7QR4 C    6 G   31'}    {'CCACAGCAGAAG*CAG'}

pCalculateTransitions:  processing IL_84694.2
  Columns 1 through 5

    {'> IL_84694.2  8…'}    {'CUGAACUU*AUCAAU…'}    {'> IL_84694.2  8…'}    {'CUGAACUU*AUCAAU…'}    {'> IL_84694.2  4…'}

  Column 6

    {'GAGAACUG*CUUAGU…'}

pCalculateTransitions:  processing IL_85033.2
  Columns 1 through 6

    {'> IL_85033.2  1…'}    {'GACC*GACC'}    {'> IL_85033.2  1…'}    {'GACC*GACC'}    {'> IL_85033.2  3…'}    {'GACU*ACCC'}

  Columns 7 through 12

    {'> IL_85033.2  3…'}    {'GACU*ACCC'}    {'> IL_85033.2  1…'}    {'GACC*GACC'}    {'> IL_85033.2  1…'}    {'GACC*GACC'}

  Columns 13 through 18

    {'> IL_85033.2  5…'}    {'CCCG*CCCG'}    {'> IL_85033.2  1…'}    {'GACC*GACC'}    {'> IL_85033.2  4…'}    {'CCUG*CCUG'}

  Columns 19 through 24

    {'> IL_85033.2  8…'}    {'GUUC*GUUC'}    {'> IL_85033.2  7…'}    {'CUUC*GGUG'}    {'> IL_85033.2  8…'}    {'GGAC*GGUC'}

  Columns 25 through 30

    {'> IL_85033.2  8…'}    {'GGAC*GGUC'}    {'> IL_85033.2  6…'}    {'ACCG*CCUU'}    {'> IL_85033.2  8…'}    {'AUUU*GUUU'}

  Columns 31 through 36

    {'> IL_85033.2  5…'}    {'GGAC*GGAC'}    {'> IL_85033.2  3…'}    {'CAGG*CAGG'}    {'> IL_85033.2  7…'}    {'CGGG*CGGG'}

  Columns 37 through 42

    {'> IL_85033.2  5…'}    {'GAAG*CGGC'}    {'> IL_85033.2  5…'}    {'GGAC*GGAC'}    {'> IL_85033.2  8…'}    {'UACA*UUGA'}

  Columns 43 through 48

    {'> IL_85033.2  8…'}    {'GCAC*GGAU'}    {'> IL_85033.2  3…'}    {'GGAC*GGAC'}    {'> IL_85033.2  8…'}    {'UACA*UUGA'}

  Columns 49 through 54

    {'> IL_85033.2  8…'}    {'GCAC*GGAU'}    {'> IL_85033.2  8…'}    {'AGAC*GUAU'}    {'> IL_85033.2  5…'}    {'GCAC*GCAC'}

  Columns 55 through 60

    {'> IL_85033.2  8…'}    {'AGAC*GUAU'}    {'> IL_85033.2  5…'}    {'UGGA*UAGAG'}    {'> IL_85033.2  4…'}    {'UGGU*GAGAG'}

  Columns 61 through 66

    {'> IL_85033.2  1…'}    {'UGGU*GAGAG'}    {'> IL_85033.2  1…'}    {'UGGU*GAGAG'}    {'> IL_85033.2  8…'}    {'CGGGG*CAAG'}

  Columns 67 through 70

    {'> IL_85033.2  8…'}    {'CGGGG*CAAG'}    {'> IL_85033.2  1…'}    {'UGGU*GAGAG'}

pCalculateTransitions:  processing IL_85222.1
    {'> IL_85222.1  4LFB G 1124 C 1149'}    {'GUUGCGGC*ACUC'}

pCalculateTransitions:  processing IL_85498.1
    {'> IL_85498.1  8VVJ U   11 G   35'}    {'UGGCGAACAG*CGG'}

pCalculateTransitions:  processing IL_85536.2
  Columns 1 through 6

    {'> IL_85536.2  8…'}    {'GGGAUA*UUCAAC'}    {'> IL_85536.2  8…'}    {'GGGAUA*UUCAAC'}    {'> IL_85536.2  4…'}    {'CGGAUU*AUGAAG'}

  Columns 7 through 12

    {'> IL_85536.2  5…'}    {'CGGAUU*AUGAAG'}    {'> IL_85536.2  8…'}    {'CGGAUG*CUGAUG'}    {'> IL_85536.2  8…'}    {'CGGAUG*CUGAUG'}

  Columns 13 through 16

    {'> IL_85536.2  8…'}    {'GCUAAC*GCGAAC'}    {'> IL_85536.2  6…'}    {'UAAUCAC*GGAACUG'}

pCalculateTransitions:  processing IL_85599.2
  Columns 1 through 6

    {'> IL_85599.2  5…'}    {'UAG*UGGG'}    {'> IL_85599.2  8…'}    {'UAG*UGGG'}    {'> IL_85599.2  7…'}    {'UAG*CGGG'}

  Columns 7 through 12

    {'> IL_85599.2  8…'}    {'UAG*UGGG'}    {'> IL_85599.2  4…'}    {'UAG*CGGG'}    {'> IL_85599.2  9…'}    {'CAG*UGGG'}

  Columns 13 through 18

    {'> IL_85599.2  9…'}    {'CAG*CGGG'}    {'> IL_85599.2  4…'}    {'CAG*CGGG'}    {'> IL_85599.2  1…'}    {'UAU*AGG'}

pCalculateTransitions:  processing IL_85630.1
    {'> IL_85630.1  4LVW G    4 C   85'}    {'GAGUAGUGC*AUCCGC'}

pCalculateTransitions:  processing IL_85652.1
    {'> IL_85652.1  1MFQ U  181 A  216'}    {'UGAACCG*CAAAA'}

pCalculateTransitions:  processing IL_85879.1
    {'> IL_85879.1  8CRE G  513 C  571'}    {'GGAUAAUGGC*GACGAUAC'}

pCalculateTransitions:  processing IL_86012.1
    {'> IL_86012.1  8P9A U 1272 G 1438'}    {'UGCAUGGU*CUGUGAUG'}

pCalculateTransitions:  processing IL_86136.1
    {'> IL_86136.1  8CRE G  512 C  541'}    {'GAGCGAGG*AAC'}

pCalculateTransitions:  processing IL_87211.1
    {'> IL_87211.1  5J7L U 1415 G 1587'}    {'UGCAUC*AG'}

pCalculateTransitions:  processing IL_87284.1
    {'> IL_87284.1  1…'}    {'UCACAG*UCACAG'}    {'> IL_87284.1  1…'}    {'UCACAG*UCACAG'}    {'> IL_87284.1  2…'}    {'CGAAAG*CGAAAG'}

pCalculateTransitions:  processing IL_87290.1
    {'> IL_87290.1  5J7L G 2124 C 2174'}    {'GGAGGCCGACCUUGAA*AUAC'}

pCalculateTransitions:  processing IL_87907.2
  Columns 1 through 6

    {'> IL_87907.2  6…'}    {'GAC*GCC'}    {'> IL_87907.2  8…'}    {'AAC*GCU'}    {'> IL_87907.2  8…'}    {'AAC*GCU'}

  Columns 7 through 12

    {'> IL_87907.2  8…'}    {'AAC*GCU'}    {'> IL_87907.2  8…'}    {'AAC*GCU'}    {'> IL_87907.2  8…'}    {'CAC*GCG'}

  Columns 13 through 18

    {'> IL_87907.2  6…'}    {'GAG*CCC'}    {'> IL_87907.2  5…'}    {'GAC*GCC'}    {'> IL_87907.2  1…'}    {'ACU*ACU'}

  Columns 19 through 24

    {'> IL_87907.2  4…'}    {'CUG*CUG'}    {'> IL_87907.2  6…'}    {'GAG*CCC'}    {'> IL_87907.2  3…'}    {'CUG*CUG'}

  Columns 25 through 30

    {'> IL_87907.2  3…'}    {'GCC*GCC'}    {'> IL_87907.2  6…'}    {'GAG*CCC'}    {'> IL_87907.2  5…'}    {'AAU*ACU'}

  Columns 31 through 36

    {'> IL_87907.2  7…'}    {'CCG*CCG'}    {'> IL_87907.2  4…'}    {'GAU*GCC'}    {'> IL_87907.2  5…'}    {'CUG*CUG'}

  Columns 37 through 42

    {'> IL_87907.2  7…'}    {'GCC*GCC'}    {'> IL_87907.2  4…'}    {'CCG*CCG'}    {'> IL_87907.2  3…'}    {'CUG*CUG'}

  Columns 43 through 48

    {'> IL_87907.2  1…'}    {'GAA*UCC'}    {'> IL_87907.2  7…'}    {'CCG*CCG'}    {'> IL_87907.2  4…'}    {'CUG*CUG'}

  Columns 49 through 54

    {'> IL_87907.2  3…'}    {'CUG*CUG'}    {'> IL_87907.2  1…'}    {'AAU*ACU'}    {'> IL_87907.2  3…'}    {'CUG*CUG'}

  Columns 55 through 60

    {'> IL_87907.2  5…'}    {'CUG*CUG'}    {'> IL_87907.2  4…'}    {'CUG*CUG'}    {'> IL_87907.2  6…'}    {'GAG*CCC'}

  Columns 61 through 66

    {'> IL_87907.2  1…'}    {'CAC*GCG'}    {'> IL_87907.2  1…'}    {'GAG*CCU'}    {'> IL_87907.2  3…'}    {'CUG*CUG'}

  Columns 67 through 72

    {'> IL_87907.2  8…'}    {'CAU*GCG'}    {'> IL_87907.2  5…'}    {'CUG*CUG'}    {'> IL_87907.2  2…'}    {'UUA*UUA'}

  Columns 73 through 78

    {'> IL_87907.2  5…'}    {'GAU*ACC'}    {'> IL_87907.2  4…'}    {'CAG*CCG'}    {'> IL_87907.2  8…'}    {'CAU*GCG'}

  Columns 79 through 84

    {'> IL_87907.2  4…'}    {'GUC*GUC'}    {'> IL_87907.2  7…'}    {'CCG*CCG'}    {'> IL_87907.2  4…'}    {'CCU*ACG'}

  Columns 85 through 90

    {'> IL_87907.2  1…'}    {'AAU*ACU'}    {'> IL_87907.2  3…'}    {'CUG*CUG'}    {'> IL_87907.2  4…'}    {'CAC*GCG'}

  Columns 91 through 96

    {'> IL_87907.2  4…'}    {'CUG*CUG'}    {'> IL_87907.2  5…'}    {'CUG*CUG'}    {'> IL_87907.2  3…'}    {'CUG*CUG'}

  Columns 97 through 102

    {'> IL_87907.2  3…'}    {'CUG*CUG'}    {'> IL_87907.2  5…'}    {'CAC*GCG'}    {'> IL_87907.2  1…'}    {'CUG*CUG'}

  Columns 103 through 108

    {'> IL_87907.2  5…'}    {'ACU*ACU'}    {'> IL_87907.2  6…'}    {'GCC*GCC'}    {'> IL_87907.2  4…'}    {'ACG*CCU'}

  Columns 109 through 114

    {'> IL_87907.2  8…'}    {'ACG*CCU'}    {'> IL_87907.2  7…'}    {'GUC*GUC'}    {'> IL_87907.2  7…'}    {'GAG*CCC'}

  Columns 115 through 120

    {'> IL_87907.2  4…'}    {'CUG*CUG'}    {'> IL_87907.2  4…'}    {'CUG*CUG'}    {'> IL_87907.2  4…'}    {'CCG*CCG'}

  Columns 121 through 126

    {'> IL_87907.2  7…'}    {'GUC*GUC'}    {'> IL_87907.2  9…'}    {'GAG*CCC'}    {'> IL_87907.2  4…'}    {'CUG*CUG'}

  Columns 127 through 132

    {'> IL_87907.2  5…'}    {'ACU*ACU'}    {'> IL_87907.2  7…'}    {'UCG*CAA'}    {'> IL_87907.2  4…'}    {'CCG*CCG'}

  Columns 133 through 138

    {'> IL_87907.2  9…'}    {'UCC*GAG'}    {'> IL_87907.2  1…'}    {'CCG*CCG'}    {'> IL_87907.2  4…'}    {'CUG*CUG'}

  Columns 139 through 144

    {'> IL_87907.2  4…'}    {'CCU*AAG'}    {'> IL_87907.2  3…'}    {'CUG*CUG'}    {'> IL_87907.2  7…'}    {'ACA*UCU'}

  Columns 145 through 150

    {'> IL_87907.2  7…'}    {'CUG*CUG'}    {'> IL_87907.2  4…'}    {'GCC*GCC'}    {'> IL_87907.2  8…'}    {'GUC*GUU'}

  Columns 151 through 156

    {'> IL_87907.2  1…'}    {'CUG*CUG'}    {'> IL_87907.2  7…'}    {'CUG*CUG'}    {'> IL_87907.2  8…'}    {'AUA*UCU'}

  Columns 157 through 162

    {'> IL_87907.2  8…'}    {'GAU*ACC'}    {'> IL_87907.2  4…'}    {'GUC*GUC'}    {'> IL_87907.2  4…'}    {'GUC*GUC'}

  Columns 163 through 168

    {'> IL_87907.2  1…'}    {'UCA*UCA'}    {'> IL_87907.2  7…'}    {'UCC*GAG'}    {'> IL_87907.2  8…'}    {'GUC*GUU'}

  Columns 169 through 174

    {'> IL_87907.2  7…'}    {'CUA*UCG'}    {'> IL_87907.2  4…'}    {'CUG*CCG'}    {'> IL_87907.2  8…'}    {'GCU*GUC'}

  Columns 175 through 180

    {'> IL_87907.2  7…'}    {'AAU*ACU'}    {'> IL_87907.2  8…'}    {'GUC*GUC'}    {'> IL_87907.2  4…'}    {'CAG*CCG'}

  Columns 181 through 186

    {'> IL_87907.2  4…'}    {'GUC*GUC'}    {'> IL_87907.2  4…'}    {'CGU*GAG'}    {'> IL_87907.2  7…'}    {'GUC*GCC'}

  Columns 187 through 192

    {'> IL_87907.2  9…'}    {'CUG*CCG'}    {'> IL_87907.2  7…'}    {'CAU*ACG'}    {'> IL_87907.2  7…'}    {'AAU*ACU'}

  Columns 193 through 198

    {'> IL_87907.2  7…'}    {'GUC*GCC'}    {'> IL_87907.2  8…'}    {'GAU*ACC'}    {'> IL_87907.2  7…'}    {'GAC*GCC'}

  Columns 199 through 204

    {'> IL_87907.2  5…'}    {'CUG*CCG'}    {'> IL_87907.2  4…'}    {'GUC*GUC'}    {'> IL_87907.2  5…'}    {'GUC*GUC'}

  Columns 205 through 210

    {'> IL_87907.2  8…'}    {'GCU*GUC'}    {'> IL_87907.2  5…'}    {'AAU*ACU'}    {'> IL_87907.2  4…'}    {'CUU*ACG'}

  Columns 211 through 216

    {'> IL_87907.2  5…'}    {'UCA*UCA'}    {'> IL_87907.2  4…'}    {'GUC*GUC'}    {'> IL_87907.2  4…'}    {'CUG*CCG'}

  Columns 217 through 222

    {'> IL_87907.2  8…'}    {'GUG*CUU'}    {'> IL_87907.2  7…'}    {'GAC*GCC'}    {'> IL_87907.2  5…'}    {'GAC*GAC'}

  Columns 223 through 228

    {'> IL_87907.2  4…'}    {'CCC*GUG'}    {'> IL_87907.2  8…'}    {'CUG*CCG'}    {'> IL_87907.2  8…'}    {'AUU*ACU'}

  Columns 229 through 234

    {'> IL_87907.2  1…'}    {'GUC*GUC'}    {'> IL_87907.2  8…'}    {'CUG*CCG'}    {'> IL_87907.2  8…'}    {'CUG*CCG'}

  Columns 235 through 240

    {'> IL_87907.2  1…'}    {'CAA*UCG'}    {'> IL_87907.2  1…'}    {'AAU*ACU'}    {'> IL_87907.2  8…'}    {'GUC*GUC'}

  Columns 241 through 246

    {'> IL_87907.2  1…'}    {'AAU*ACU'}    {'> IL_87907.2  8…'}    {'CUG*CCG'}    {'> IL_87907.2  5…'}    {'GGC*GGC'}

  Columns 247 through 252

    {'> IL_87907.2  8…'}    {'AUA*UCU'}    {'> IL_87907.2  7…'}    {'GCC*GCC'}    {'> IL_87907.2  4…'}    {'GAC*GGC'}

  Columns 253 through 258

    {'> IL_87907.2  8…'}    {'GAU*AAC'}    {'> IL_87907.2  8…'}    {'GCG*CCU'}    {'> IL_87907.2  4…'}    {'GUC*GUC'}

  Columns 259 through 264

    {'> IL_87907.2  5…'}    {'CAC*GGAG'}    {'> IL_87907.2  8…'}    {'GCU*GAU'}    {'> IL_87907.2  7…'}    {'GCC*GUC'}

  Columns 265 through 270

    {'> IL_87907.2  4…'}    {'ACG*CAU'}    {'> IL_87907.2  8…'}    {'UAC*GAA'}    {'> IL_87907.2  4…'}    {'GCC*GUC'}

  Columns 271 through 276

    {'> IL_87907.2  8…'}    {'CGA*UAG'}    {'> IL_87907.2  1…'}    {'CAC*GGGG'}    {'> IL_87907.2  3…'}    {'GGG*CAC'}

  Columns 277 through 282

    {'> IL_87907.2  5…'}    {'GGC*GGC'}    {'> IL_87907.2  8…'}    {'GUG*CUU'}    {'> IL_87907.2  8…'}    {'CGA*UAG'}

  Columns 283 through 288

    {'> IL_87907.2  3…'}    {'CUG*CCG'}    {'> IL_87907.2  8…'}    {'GAC*GGC'}    {'> IL_87907.2  5…'}    {'UAG*CGA'}

  Columns 289 through 294

    {'> IL_87907.2  7…'}    {'GAC*GCC'}    {'> IL_87907.2  2…'}    {'GGG*CAC'}    {'> IL_87907.2  3…'}    {'GGG*CAC'}

  Columns 295 through 300

    {'> IL_87907.2  3…'}    {'AAC*GGU'}    {'> IL_87907.2  7…'}    {'CCG*CCG'}    {'> IL_87907.2  4…'}    {'CAG*CAG'}

  Columns 301 through 306

    {'> IL_87907.2  8…'}    {'GAC*GGC'}    {'> IL_87907.2  4…'}    {'UAG*CGA'}    {'> IL_87907.2  8…'}    {'AUU*ACU'}

  Columns 307 through 312

    {'> IL_87907.2  8…'}    {'GCG*CCU'}    {'> IL_87907.2  4…'}    {'GAC*GGC'}    {'> IL_87907.2  8…'}    {'GAU*AGC'}

  Columns 313 through 318

    {'> IL_87907.2  8…'}    {'UAU*AGA'}    {'> IL_87907.2  8…'}    {'CAU*AGUG'}    {'> IL_87907.2  8…'}    {'CAU*AGUG'}

  Columns 319 through 324

    {'> IL_87907.2  8…'}    {'GAU*AAC'}    {'> IL_87907.2  8…'}    {'CAC*GGG'}    {'> IL_87907.2  3…'}    {'CAG*UGG'}

  Columns 325 through 330

    {'> IL_87907.2  4…'}    {'UAG*CGA'}    {'> IL_87907.2  8…'}    {'UAC*GAA'}    {'> IL_87907.2  5…'}    {'CAU*GGG'}

  Columns 331 through 336

    {'> IL_87907.2  7…'}    {'CAG*CAG'}    {'> IL_87907.2  4…'}    {'GUC*GUC'}    {'> IL_87907.2  3…'}    {'AAC*GGU'}

  Columns 337 through 342

    {'> IL_87907.2  8…'}    {'UAU*AGA'}    {'> IL_87907.2  8…'}    {'GGC*GAC'}    {'> IL_87907.2  7…'}    {'CGG*UAG'}

  Columns 343 through 348

    {'> IL_87907.2  4…'}    {'CAU*GGG'}    {'> IL_87907.2  8…'}    {'CGA*UGG'}    {'> IL_87907.2  8…'}    {'ACG*CCU'}

  Columns 349 through 354

    {'> IL_87907.2  4…'}    {'CGG*CAG'}    {'> IL_87907.2  1…'}    {'CAC*GAGG'}    {'> IL_87907.2  1…'}    {'UAU*AGG'}

  Columns 355 through 358

    {'> IL_87907.2  5…'}    {'UAG*CAG'}    {'> IL_87907.2  8…'}    {'CUAC*GAG'}

pCalculateTransitions:  processing IL_88017.1
  Columns 1 through 6

    {'> IL_88017.1  7…'}    {'GAACUAC*GC'}    {'> IL_88017.1  7…'}    {'GAACUAC*GC'}    {'> IL_88017.1  3…'}    {'GAACUAC*GC'}

  Columns 7 through 12

    {'> IL_88017.1  7…'}    {'GAACUAC*GC'}    {'> IL_88017.1  7…'}    {'GAACUAC*GC'}    {'> IL_88017.1  2…'}    {'GAACUAC*GC'}

  Columns 13 through 14

    {'> IL_88017.1  6…'}    {'GAACUAC*GC'}

pCalculateTransitions:  processing IL_88072.1
    {'> IL_88072.1  4FRG A    6 U   78'}    {'AAAAGCAUAG*CCU'}

pCalculateTransitions:  processing IL_88082.1
    {'> IL_88082.1  8P9A G   42…'}    {'GAUUAAG*CGC'}    {'> IL_88082.1  8CRE G   42…'}    {'GAUUAAG*CGC'}

pCalculateTransitions:  processing IL_88116.2
  Columns 1 through 5

    {'> IL_88116.2  8…'}    {'UCAAAGU*AACCAAG'}    {'> IL_88116.2  8…'}    {'UCAAAGU*AACCAAG'}    {'> IL_88116.2  4…'}

  Column 6

    {'UGAACAC*GACGAAG'}

pCalculateTransitions:  processing IL_88269.4
    {'> IL_88269.4  4…'}    {'GGACGC*GGUAC'}    {'> IL_88269.4  5…'}    {'UGAAAAAGUGAUGUA…'}    {'> IL_88269.4  5…'}    {'GGAGGC*GUUAC'}

pCalculateTransitions:  processing IL_88974.1
    {'> IL_88974.1  7JRT U   77…'}    {'UCGCGAGCAC*GGA'}    {'> IL_88974.1  7JRT U   77…'}    {'UCGCGAGCAC*GGA'}

pCalculateTransitions:  processing IL_89021.2
  Columns 1 through 6

    {'> IL_89021.2  4…'}    {'CUAAG*CGAUG'}    {'> IL_89021.2  7…'}    {'CUAAG*CGAUG'}    {'> IL_89021.2  5…'}    {'CUAAG*CGAUG'}

  Columns 7 through 12

    {'> IL_89021.2  9…'}    {'UCAAG*CGAAG'}    {'> IL_89021.2  7…'}    {'UCAAG*UGAAG'}    {'> IL_89021.2  4…'}    {'UUAAG*CGAAG'}

pCalculateTransitions:  processing IL_89047.1
    {'> IL_89047.1  8CRE U  878 A  904'}    {'UUGUCAGCU*UGGAUUUA'}

pCalculateTransitions:  processing IL_89099.1
    {'> IL_89099.1  1D4R G   12 C   17'}    {'GGGAGC*GGGAGC'}

pCalculateTransitions:  processing IL_89312.1
    {'> IL_89312.1  3IGI C   76 G  111'}    {'CAAGUG*GAAG'}

pCalculateTransitions:  processing IL_89505.4
  Columns 1 through 6

    {'> IL_89505.4  8…'}    {'GUC*GC'}    {'> IL_89505.4  8…'}    {'GUC*GC'}    {'> IL_89505.4  8…'}    {'AUC*GU'}

  Columns 7 through 12

    {'> IL_89505.4  8…'}    {'GUU*AC'}    {'> IL_89505.4  6…'}    {'GUU*AC'}    {'> IL_89505.4  8…'}    {'GUG*CC'}

  Columns 13 through 18

    {'> IL_89505.4  8…'}    {'GUU*AC'}    {'> IL_89505.4  9…'}    {'GUG*CC'}    {'> IL_89505.4  7…'}    {'GUA*UC'}

  Columns 19 through 24

    {'> IL_89505.4  5…'}    {'UUG*CA'}    {'> IL_89505.4  8…'}    {'UUA*UA'}    {'> IL_89505.4  8…'}    {'GUG*CC'}

  Columns 25 through 30

    {'> IL_89505.4  8…'}    {'UUA*UA'}    {'> IL_89505.4  8…'}    {'GUG*CC'}    {'> IL_89505.4  9…'}    {'GUC*GC'}

  Columns 31 through 36

    {'> IL_89505.4  3…'}    {'CUG*CG'}    {'> IL_89505.4  7…'}    {'GUG*CC'}    {'> IL_89505.4  4…'}    {'UUC*GA'}

  Columns 37 through 42

    {'> IL_89505.4  4…'}    {'GUG*CC'}    {'> IL_89505.4  2…'}    {'GUC*GC'}    {'> IL_89505.4  8…'}    {'AUG*CU'}

  Columns 43 through 48

    {'> IL_89505.4  3…'}    {'GUG*CC'}    {'> IL_89505.4  5…'}    {'GUG*CC'}    {'> IL_89505.4  7…'}    {'GUG*CC'}

  Columns 49 through 54

    {'> IL_89505.4  8…'}    {'AUC*GU'}    {'> IL_89505.4  8…'}    {'AUC*GU'}    {'> IL_89505.4  4…'}    {'GUG*CC'}

  Columns 55 through 60

    {'> IL_89505.4  5…'}    {'GUC*GC'}    {'> IL_89505.4  4…'}    {'GUG*CC'}    {'> IL_89505.4  4…'}    {'AUG*CU'}

  Columns 61 through 66

    {'> IL_89505.4  2…'}    {'GUU*AC'}    {'> IL_89505.4  6…'}    {'UUC*GG'}    {'> IL_89505.4  8…'}    {'AUC*GU'}

  Columns 67 through 72

    {'> IL_89505.4  5…'}    {'GUG*CC'}    {'> IL_89505.4  4…'}    {'AUA*UU'}    {'> IL_89505.4  2…'}    {'GUU*AC'}

  Columns 73 through 78

    {'> IL_89505.4  8…'}    {'GUG*CC'}    {'> IL_89505.4  8…'}    {'GUA*UC'}    {'> IL_89505.4  8…'}    {'GUG*CC'}

  Columns 79 through 84

    {'> IL_89505.4  2…'}    {'GUG*UC'}    {'> IL_89505.4  8…'}    {'GUA*UC'}    {'> IL_89505.4  5…'}    {'GUC*GC'}

  Columns 85 through 90

    {'> IL_89505.4  8…'}    {'GUA*UC'}    {'> IL_89505.4  4…'}    {'CUG*CG'}    {'> IL_89505.4  4…'}    {'GUG*CC'}

  Columns 91 through 96

    {'> IL_89505.4  3…'}    {'GUG*UC'}    {'> IL_89505.4  8…'}    {'GUA*UC'}    {'> IL_89505.4  4…'}    {'GUG*CC'}

  Columns 97 through 102

    {'> IL_89505.4  3…'}    {'GUA*UC'}    {'> IL_89505.4  8…'}    {'AUA*UU'}    {'> IL_89505.4  7…'}    {'AUA*UU'}

  Columns 103 through 108

    {'> IL_89505.4  8…'}    {'GUA*UC'}    {'> IL_89505.4  6…'}    {'AUC*GU'}    {'> IL_89505.4  3…'}    {'CUC*GG'}

  Columns 109 through 114

    {'> IL_89505.4  6…'}    {'UUC*GG'}    {'> IL_89505.4  6…'}    {'AUC*GU'}    {'> IL_89505.4  8…'}    {'GUG*CC'}

  Columns 115 through 120

    {'> IL_89505.4  6…'}    {'AUC*GU'}    {'> IL_89505.4  2…'}    {'GUG*CC'}    {'> IL_89505.4  4…'}    {'GUC*GC'}

  Columns 121 through 126

    {'> IL_89505.4  4…'}    {'GUC*GC'}    {'> IL_89505.4  2…'}    {'GUU*AC'}    {'> IL_89505.4  5…'}    {'UUG*UG'}

  Columns 127 through 132

    {'> IL_89505.4  7…'}    {'AUG*CU'}    {'> IL_89505.4  8…'}    {'UUG*UA'}    {'> IL_89505.4  8…'}    {'UUG*UA'}

  Columns 133 through 138

    {'> IL_89505.4  3…'}    {'UUC*GG'}    {'> IL_89505.4  4…'}    {'GUG*CC'}    {'> IL_89505.4  3…'}    {'GUU*AC'}

  Columns 139 through 144

    {'> IL_89505.4  8…'}    {'GUU*AC'}    {'> IL_89505.4  8…'}    {'GUU*AC'}    {'> IL_89505.4  8…'}    {'GUG*CC'}

  Columns 145 through 150

    {'> IL_89505.4  8…'}    {'CUG*CG'}    {'> IL_89505.4  8…'}    {'CUG*CG'}    {'> IL_89505.4  7…'}    {'UUU*AG'}

  Columns 151 through 156

    {'> IL_89505.4  6…'}    {'UUC*GA'}    {'> IL_89505.4  7…'}    {'AUA*UU'}    {'> IL_89505.4  8…'}    {'UUG*CG'}

  Columns 157 through 162

    {'> IL_89505.4  8…'}    {'UUG*CG'}    {'> IL_89505.4  8…'}    {'CUG*CG'}    {'> IL_89505.4  8…'}    {'GUG*CC'}

  Columns 163 through 168

    {'> IL_89505.4  8…'}    {'GUC*GC'}    {'> IL_89505.4  4…'}    {'AUU*AU'}    {'> IL_89505.4  5…'}    {'GUC*GC'}

  Columns 169 through 174

    {'> IL_89505.4  7…'}    {'GUC*GC'}    {'> IL_89505.4  7…'}    {'GUC*GC'}    {'> IL_89505.4  7…'}    {'GUC*GC'}

  Columns 175 through 180

    {'> IL_89505.4  5…'}    {'GUC*GC'}    {'> IL_89505.4  7…'}    {'GUC*GC'}    {'> IL_89505.4  7…'}    {'GUC*GC'}

  Columns 181 through 186

    {'> IL_89505.4  5…'}    {'GUC*GC'}    {'> IL_89505.4  6…'}    {'AUG*CU'}    {'> IL_89505.4  8…'}    {'GUG*CC'}

  Columns 187 through 192

    {'> IL_89505.4  8…'}    {'GUC*GC'}    {'> IL_89505.4  8…'}    {'AUU*AU'}    {'> IL_89505.4  8…'}    {'AUU*AU'}

  Columns 193 through 198

    {'> IL_89505.4  8…'}    {'GUA*UC'}    {'> IL_89505.4  5…'}    {'GUC*GC'}    {'> IL_89505.4  8…'}    {'UUG*CG'}

  Columns 199 through 204

    {'> IL_89505.4  2…'}    {'CUG*CG'}    {'> IL_89505.4  6…'}    {'GUG*CC'}    {'> IL_89505.4  2…'}    {'GUG*CC'}

  Columns 205 through 210

    {'> IL_89505.4  5…'}    {'UUC*GG'}    {'> IL_89505.4  4…'}    {'GUA*UC'}    {'> IL_89505.4  3…'}    {'UUC*GG'}

  Columns 211 through 216

    {'> IL_89505.4  4…'}    {'UUC*GG'}    {'> IL_89505.4  8…'}    {'GUG*CC'}    {'> IL_89505.4  4…'}    {'CUG*CG'}

  Columns 217 through 222

    {'> IL_89505.4  1…'}    {'GUG*CC'}    {'> IL_89505.4  3…'}    {'GUG*CC'}    {'> IL_89505.4  8…'}    {'UUG*CG'}

  Columns 223 through 228

    {'> IL_89505.4  1…'}    {'AUG*CU'}    {'> IL_89505.4  1…'}    {'AUG*CU'}    {'> IL_89505.4  5…'}    {'CUG*CG'}

  Columns 229 through 234

    {'> IL_89505.4  7…'}    {'UUC*GA'}    {'> IL_89505.4  3…'}    {'CUC*GG'}    {'> IL_89505.4  3…'}    {'CUC*GG'}

pCalculateTransitions:  processing IL_89984.3
    {'> IL_89984.3  8SYK G   12…'}    {'GUACA*UUC'}    {'> IL_89984.3  2OEU G    5…'}    {'GUACU*AUC'}

pCalculateTransitions:  processing IL_90346.1
    {'> IL_90346.1  7KVT G   47 C   72'}    {'GAAGCUA*AGC'}

pCalculateTransitions:  processing IL_90351.1
  Columns 1 through 6

    {'> IL_90351.1  2…'}    {'CACG*AAG'}    {'> IL_90351.1  5…'}    {'CACG*AAG'}    {'> IL_90351.1  5…'}    {'CGGC*GAG'}

  Columns 7 through 12

    {'> IL_90351.1  8…'}    {'CGCGCGUAAG*AUG'}    {'> IL_90351.1  4…'}    {'GAAU*CUC'}    {'> IL_90351.1  8…'}    {'GUAU*AAC'}

  Columns 13 through 16

    {'> IL_90351.1  9…'}    {'GCUA*AAC'}    {'> IL_90351.1  3…'}    {'CACG*AUGG'}

pCalculateTransitions:  processing IL_90729.1
  Columns 1 through 6

    {'> IL_90729.1  4…'}    {'CCG*AG'}    {'> IL_90729.1  5…'}    {'CCG*AG'}    {'> IL_90729.1  9…'}    {'CCG*AG'}

  Columns 7 through 12

    {'> IL_90729.1  7…'}    {'ACG*AU'}    {'> IL_90729.1  7…'}    {'CUA*AG'}    {'> IL_90729.1  8…'}    {'CCG*AG'}

  Columns 13 through 18

    {'> IL_90729.1  8…'}    {'CCG*AG'}    {'> IL_90729.1  4…'}    {'CCG*AG'}    {'> IL_90729.1  8…'}    {'CCG*UG'}

  Columns 19 through 24

    {'> IL_90729.1  7…'}    {'UGUAUC*UA'}    {'> IL_90729.1  8…'}    {'CCG*UG'}    {'> IL_90729.1  5…'}    {'CCG*AG'}

  Columns 25 through 30

    {'> IL_90729.1  9…'}    {'CCG*AG'}    {'> IL_90729.1  8…'}    {'UGUAAC*AA'}    {'> IL_90729.1  7…'}    {'CCG*AG'}

  Columns 31 through 36

    {'> IL_90729.1  8…'}    {'CUA*UG'}    {'> IL_90729.1  7…'}    {'AUA*CU'}    {'> IL_90729.1  8…'}    {'CGC*CG'}

  Columns 37 through 42

    {'> IL_90729.1  8…'}    {'CGC*UG'}    {'> IL_90729.1  4…'}    {'CUA*UG'}    {'> IL_90729.1  5…'}    {'GCG*UC'}

  Columns 43 through 48

    {'> IL_90729.1  4…'}    {'CCG*AG'}    {'> IL_90729.1  4…'}    {'CCCGGG*GG'}    {'> IL_90729.1  8…'}    {'GCGCCUG*UCC'}

  Columns 49 through 54

    {'> IL_90729.1  6…'}    {'UGC*UA'}    {'> IL_90729.1  2…'}    {'UGC*UA'}    {'> IL_90729.1  4…'}    {'UGUAAC*AA'}

  Columns 55 through 60

    {'> IL_90729.1  3…'}    {'UGC*AA'}    {'> IL_90729.1  7…'}    {'UGU*UA'}    {'> IL_90729.1  5…'}    {'AUAUUAA*AUU'}

pCalculateTransitions:  processing IL_91592.1
    {'> IL_91592.1  5U3G C   60…'}    {'CACGGCG*CGG'}    {'> IL_91592.1  7MLW C  104…'}    {'CACGGAG*CGG'}

pCalculateTransitions:  processing IL_91636.1
    {'> IL_91636.1  3KTW G  193 C  227'}    {'GGGAACC*GUGC'}

pCalculateTransitions:  processing IL_91698.1
    {'> IL_91698.1  8P9A G 1480…'}    {'GCCAGCGAU*UGUGAAAC'}    {'> IL_91698.1  8CRE G 1466…'}    {'GCCAGCGAU*UGUGAAAC'}

pCalculateTransitions:  processing IL_91920.1
    {'> IL_91920.1  5J7L G 1202 C 1243'}    {'GUAAG*UAUC'}

pCalculateTransitions:  processing IL_92446.2
  Columns 1 through 6

    {'> IL_92446.2  1…'}    {'GUUGC*AUC'}    {'> IL_92446.2  5…'}    {'GUUGC*AUC'}    {'> IL_92446.2  6…'}    {'GUUGC*AUC'}

  Columns 7 through 10

    {'> IL_92446.2  4…'}    {'GUGAU*ACC'}    {'> IL_92446.2  5…'}    {'GUUGC*AUC'}

pCalculateTransitions:  processing IL_92634.2
    {'> IL_92634.2  8…'}    {'AUAGU*GU'}    {'> IL_92634.2  8…'}    {'AUAGU*GU'}    {'> IL_92634.2  4…'}    {'AGCAA*GU'}

pCalculateTransitions:  processing IL_93889.1
    {'> IL_93889.1  4MGN U   14 G   91'}    {'UCAAUAGUAGU*GAAACGGCAG'}

pCalculateTransitions:  processing IL_94351.1
    {'> IL_94351.1  1OOA C    5 G   25'}    {'CUUGAA*UGGCG'}

pCalculateTransitions:  processing IL_94684.1
    {'> IL_94684.1  8CRE C 1375…'}    {'CUAUGG*AAG'}    {'> IL_94684.1  8P9A C 1389…'}    {'CUAUGG*AAG'}

pCalculateTransitions:  processing IL_94910.1
  Columns 1 through 5

    {'> IL_94910.1  7…'}    {'ACGAGCU*UUGACU'}    {'> IL_94910.1  4…'}    {'GCAAGUG*AUGACC'}    {'> IL_94910.1  4…'}

  Column 6

    {'CCGAGUG*UUUGACG'}

pCalculateTransitions:  processing IL_94967.1
    {'> IL_94967.1  6JOO G   57 C   65'}    {'GCGU*UC'}

pCalculateTransitions:  processing IL_95570.1
    {'> IL_95570.1  6CK5 C   21…'}    {'CAGU*GUUCG'}    {'> IL_95570.1  4RUM C   20…'}    {'CAAU*GCAG'}

pCalculateTransitions:  processing IL_95583.2
  Columns 1 through 6

    {'> IL_95583.2  5…'}    {'CCGG*CG'}    {'> IL_95583.2  9…'}    {'CCGG*CG'}    {'> IL_95583.2  1…'}    {'CAGC*GG'}

  Columns 7 through 12

    {'> IL_95583.2  4…'}    {'CCAG*CG'}    {'> IL_95583.2  8…'}    {'CCAG*CG'}    {'> IL_95583.2  8…'}    {'CCAG*CG'}

  Columns 13 through 18

    {'> IL_95583.2  7…'}    {'CCGG*CG'}    {'> IL_95583.2  9…'}    {'GAAG*CC'}    {'> IL_95583.2  4…'}    {'UCAGC*GG'}

  Columns 19 through 22

    {'> IL_95583.2  5…'}    {'UCAUC*GG'}    {'> IL_95583.2  3…'}    {'UAAU*AG'}

pCalculateTransitions:  processing IL_95727.1
    {'> IL_95727.1  4LFB G  683 C  707'}    {'GAGUAGCG*CAGAUAC'}

pCalculateTransitions:  processing IL_95811.1
    {'> IL_95811.1  1ET4 C  211 G  230'}    {'CGCAUAAC*GCG'}

pCalculateTransitions:  processing IL_96236.1
    {'> IL_96236.1  5J7L G  930 C  848'}    {'GUUAUA*AUUC'}

pCalculateTransitions:  processing IL_96303.1
  Columns 1 through 5

    {'> IL_96303.1  8…'}    {'GUUGCGUCCGAAAG*…'}    {'> IL_96303.1  8…'}    {'GUUGCGUCCGAAAG*…'}    {'> IL_96303.1  8…'}

  Column 6

    {'GUUACGUCCGAAAG*…'}

pCalculateTransitions:  processing IL_96332.5
  Columns 1 through 6

    {'> IL_96332.5  8…'}    {'GACGGUC*GGGC'}    {'> IL_96332.5  8…'}    {'GACGGUC*GGGC'}    {'> IL_96332.5  8…'}    {'GACGGUC*GGGC'}

  Columns 7 through 12

    {'> IL_96332.5  4…'}    {'GAAGGAC*GAGC'}    {'> IL_96332.5  4…'}    {'GAAGGAC*GAGC'}    {'> IL_96332.5  7…'}    {'GAGGGUC*GGGC'}

  Columns 13 through 14

    {'> IL_96332.5  3…'}    {'CCCAGG*CAAG'}

pCalculateTransitions:  processing IL_96371.1
    {'> IL_96371.1  6CK5 U   80 G   97'}    {'UAG*CGGG'}

pCalculateTransitions:  processing IL_96759.1
    {'> IL_96759.1  5V1K C  203 G  110'}    {'CGAA*UUAG'}

pCalculateTransitions:  processing IL_96788.1
    {'> IL_96788.1  3IGI G  267 C  286'}    {'GAGGU*AAGUC'}

pCalculateTransitions:  processing IL_97273.1
    {'> IL_97273.1  8…'}    {'GGGAUC*GUC'}    {'> IL_97273.1  8…'}    {'GGGAUC*GUC'}    {'> IL_97273.1  3…'}    {'GGUGCU*AAC'}

pCalculateTransitions:  processing IL_97631.1
    {'> IL_97631.1  4V9F A  562 U  595'}    {'ACGAAU*AGACU'}

pCalculateTransitions:  processing IL_97697.1
  Columns 1 through 6

    {'> IL_97697.1  5…'}    {'AACUGAAU*ACAUU'}    {'> IL_97697.1  5…'}    {'AACUGAAU*ACAUU'}    {'> IL_97697.1  5…'}    {'AACUGAAU*ACAUU'}

  Columns 7 through 8

    {'> IL_97697.1  5…'}    {'AACUGAAU*ACAUU'}

pCalculateTransitions:  processing IL_98347.1
    {'> IL_98347.1  6RTI U   35 A   12'}    {'UACG*AAAA'}

pCalculateTransitions:  processing IL_99358.1
  Columns 1 through 6

    {'> IL_99358.1  4…'}    {'CCCG*AUG'}    {'> IL_99358.1  8…'}    {'GGCG*GUC'}    {'> IL_99358.1  7…'}    {'CUGC*CAG'}

  Columns 7 through 12

    {'> IL_99358.1  4…'}    {'CUGU*GUG'}    {'> IL_99358.1  6…'}    {'CUUA*UAG'}    {'> IL_99358.1  6…'}    {'CAGACGCCU*CCG'}

  Columns 13 through 16

    {'> IL_99358.1  4…'}    {'GAACAAGCUAG*AUC'}    {'> IL_99358.1  7…'}    {'UCGCG*AAA'}

pCalculateTransitions:  processing IL_99380.1
    {'> IL_99380.1  8CRE U  316 G  344'}    {'UUUCGA*UG'}

pCalculateTransitions:  processing IL_99498.1
    {'> IL_99498.1  3IGI G   10 C  262'}    {'GCAUG*CUUACC'}

pCalculateTransitions:  processing IL_99646.2
  Columns 1 through 6

    {'> IL_99646.2  5…'}    {'CUAU*AAAUG'}    {'> IL_99646.2  7…'}    {'CUAU*AAACG'}    {'> IL_99646.2  9…'}    {'CUAG*CGAAG'}

  Columns 7 through 12

    {'> IL_99646.2  2…'}    {'AUAG*CGAGU'}    {'> IL_99646.2  9…'}    {'AUAG*CGAAU'}    {'> IL_99646.2  4…'}    {'CUAG*CGAUG'}

pCalculateTransitions:  processing IL_99692.2
  Columns 1 through 5

    {'> IL_99692.2  5…'}    {'CCCAGACAG*UCGAG'}    {'> IL_99692.2  4…'}    {'CCUAGACAG*CCGAG'}    {'> IL_99692.2  8…'}

  Columns 6 through 10

    {'UCUAGACAG*CCGAA'}    {'> IL_99692.2  9…'}    {'CGAAGACAG*UCGAG'}    {'> IL_99692.2  8…'}    {'UCUAGACAG*CCGAA'}

  Columns 11 through 12

    {'> IL_99692.2  5…'}    {'CUAAGACAG*UCGAG'}

pCalculateTransitions:  cWW basepair probabilities for CG, GC, AU, UA, GU, UG are

cWW_M =

    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

pCalculateTransitions:  initial distribution for A, C, G, U is

initial_M =

    0.2609
    0.1476
    0.3543
    0.2372

pCalculateTransitions:  initial transition matrix is

initialTransition_M =

    0.2515    0.1805    0.3462    0.2219
    0.1989    0.1459    0.3687    0.2865
    0.3515    0.1271    0.3346    0.1868
    0.2239    0.1586    0.3675    0.2500

pCalculateTransitions:  interior transition matrix is

transition_M =

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

Timestamp 18-Jul-2025 22:46:19
pMakeSCFGModels: Making JAR3D model for motif group IL_00225.13, number 1 of 411
pMakeSCFGModels: Loaded C:\Users\zirbel\Documents\JAR3D\Motifs\IL_3.98\mat\IL_00225.13.mat, looks like:
Search = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

         motif_id: 'IL_00225.13'
       Candidates: [49×6 uint16]
    consensusEdge: [5×5 double]
     bp_signature: 'cWW-L-cWW'
        Signature: 'cWW-L-cWW'
       chainbreak: {'3'}
         loop_ids: {49×1 cell}
         Truncate: 4
            Query: [1×1 struct]
       MaxDiffMat: [1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Inf]
             File: [1×49 struct]
         NumFixed: 0


ans = 

  1×49 <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> array with fields:

    Backbone
    BasePhosphate
    BaseRibose
    BestChains
    CI
    ClassVersion
    Comment
    Coplanar
    Covalent
    Crossing
    Distance
    Edge
    Filename
    Flank
    HandClass
    Info
    LongestChain
    Modified
    NT
    NumNT
    PDBFilename
    PDBID
    Range
    Redundant


ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

         Backbone: [5×5 double]
    BasePhosphate: [5×5 double]
       BaseRibose: [5×5 double]
       BestChains: {{1×1 cell}}
               CI: []
     ClassVersion: 8
          Comment: []
         Coplanar: [5×5 double]
         Covalent: [5×5 double]
         Crossing: [5×5 double]
         Distance: []
             Edge: [51×52 double]
         Filename: '6TFF'
            Flank: [5×5 double]
        HandClass: []
             Info: [1×1 struct]
     LongestChain: [1 52]
         Modified: 0
               NT: [1×5 struct]
            NumNT: 5
      PDBFilename: '6TFF.pdb'
            PDBID: '6TFF'
            Range: [5×5 double]
        Redundant: [5×5 double]

pMakeNodes starting loop:     a=6TFF|1|A|C|37 B=6TFF|1|A|G|23
  2 Basepair    37   23 CG cWW 
pMakeNodes probe for inserts:  a=6TFF|1|A|G|38 B=6TFF|1|A|U|22
    Insertion on left  6TFF|1|A|G|38
pMakeNodesProbeForInsertions:  a 6TFF|1|A|A|39 interacts with 6TFF|1|A|U|22
pMakeNodesProbeForInsertions:  B 6TFF|1|A|U|22 interacts with 6TFF|1|A|A|39
pMakeNodesProbeForInsertions:  B 6TFF|1|A|U|22 interacts with 6TFF|1|A|A|39
pMakeNodes probed for insert:  a=6TFF|1|A|A|39 B=6TFF|1|A|U|22
  3 Basepair    39   22 AU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6TFF|1|A|G|23
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CG'
           RightLetter: 'G'
               Comment: ' // Basepair C37 - G23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6TFF|1|A|G|23'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A39 - U22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_00225.13_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.4465
   -3.2245
   -3.3938
   -3.2245
   -3.6472
   -3.6472
   -3.2245
   -3.2631
   -5.2582
   -3.9556
   -5.2582
   -3.9556
   -3.2245
   -3.2245
   -3.2631
   -3.7308
   -3.1718
   -3.3938
   -3.6472
   -3.9556
   -3.3938
   -3.4252
   -3.6472
   -3.4252
   -3.6472
   -3.4252
   -3.7308
   -5.4184
   -3.6845
   -5.4184
   -3.2631
   -3.7590
   -3.7590
   -3.1718
   -3.4852
   -3.6922
   -3.4852
   -4.0006
   -3.2631
   -3.1718
   -3.6845
   -3.1718
   -3.1718
   -3.1718
   -3.7372
   -3.2245
   -3.1718
   -3.7372
   -3.1718

Timestamp 18-Jul-2025 22:46:25
pMakeSCFGModels: Making JAR3D model for motif group IL_00555.1, number 2 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|A|2520 B=8P9A|1|AR|U|2587
  2 Basepair  2520 2587 AU cWW 
pMakeNodes probe for inserts:  a=8P9A|1|AR|U|2521 B=8P9A|1|AR|G|2584
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|U|2521 interacts with 8P9A|1|AR|A|2523
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|G|2584 interacts with 8P9A|1|AR|C|2526
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|G|2584 interacts with 8P9A|1|AR|C|2526
pMakeNodes probed for insert:  a=8P9A|1|AR|U|2521 B=8P9A|1|AR|G|2584
pMakeNodes making a cluster near strand break a=8P9A|1|AR|U|2521 B=8P9A|1|AR|G|2584
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 5 to 5
aa is 4 bb is 5
  3 Cluster   8P9A|1|AR|U|2521:8P9A|1|AR|C|2526 8P9A|1|AR|G|2584:8P9A|1|AR|G|2584
    LR Inter  8P9A|1|AR|C|2526 8P9A|1|AR|G|2584 cWW 
    LL Inter  8P9A|1|AR|U|2521 8P9A|1|AR|A|2523 cWS 
pMakeNodesCluster a=5 B=4 at the end
pMakeNodesCluster a=5 B=4 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2520 - U2587 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4]
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAC'
           RightLetter: 'G'
               Comment: ' // Cluster node 8P9A|1|AR|U|2521:8P9A|1|AR|C|2526 and 8P9A|1|AR|G|2584:8P9A|1|AR|G|2584'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  5 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_00555.1 allow insertions from initial node 4?
ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_00555.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.3179
   -7.3179

Timestamp 18-Jul-2025 22:46:26
pMakeSCFGModels: Making JAR3D model for motif group IL_00881.1, number 3 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|C|1582 B=9DFE|1|1A|G|1416
  2 Basepair  1582 1416 CG cWW 
pMakeNodes probe for inserts:  a=9DFE|1|1A|A|1583 B=9DFE|1|1A|U|1415
    Insertion on left  9DFE|1|1A|A|1583
    Insertion on left  9DFE|1|1A|A|1586
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|A|1587 interacts with 9DFE|1|1A|U|1415
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|U|1415 interacts with 9DFE|1|1A|A|1587
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|U|1415 interacts with 9DFE|1|1A|A|1587
pMakeNodes probed for insert:  a=9DFE|1|1A|A|1587 B=9DFE|1|1A|U|1415
  3 Basepair  1587 1415 AU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|G|1416
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|C|1582
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAA'
           RightLetter: 'G'
               Comment: ' // Basepair C1582 - G1416 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|G|1416'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|C|1582'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A1587 - U1415 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_00881.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7200
   -4.7734

Timestamp 18-Jul-2025 22:46:26
pMakeSCFGModels: Making JAR3D model for motif group IL_00981.1, number 4 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|U|1694 B=8P9A|1|AR|A|1752
  2 Basepair  1694 1752 UA cWW 
No need to probe because of interaction between a=8P9A|1|AR|U|1695 B=8P9A|1|AR|A|1750
  3 Basepair  1695 1750 UA tWH 
No need to probe because of interaction between a=8P9A|1|AR|A|1696 B=8P9A|1|AR|A|1749
  4 Basepair  1696 1749 AA tHH 
No need to probe because of interaction between a=8P9A|1|AR|A|1697 B=8P9A|1|AR|G|1748
  5 Basepair  1697 1748 AG tHS 
No need to probe because of interaction between a=8P9A|1|AR|C|1698 B=8P9A|1|AR|G|1747
  6 Basepair  1698 1747 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1694 - A1752 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1695 - A1750 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A1696 - A1749 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1697 - G1748 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1698 - G1747 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_00981.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.3867
   -4.3867

Timestamp 18-Jul-2025 22:46:27
pMakeSCFGModels: Making JAR3D model for motif group IL_01038.1, number 5 of 411
pMakeNodes starting loop:     a=3OXE|1|A|G|38 B=3OXE|1|A|C|66
  2 Basepair    38   66 GC cWW 
No need to probe because of interaction between a=3OXE|1|A|C|39 B=3OXE|1|A|A|64
  3 Basepair    39   64 CA tWH 
pMakeNodes probe for inserts:  a=3OXE|1|A|A|40 B=3OXE|1|A|A|63
    Insertion on left  3OXE|1|A|A|40
    Insertion on right 3OXE|1|A|A|63
pMakeNodesProbeForInsertions:  a 3OXE|1|A|A|41 interacts with 3OXE|1|A|G|62
pMakeNodesProbeForInsertions:  B 3OXE|1|A|G|62 interacts with 3OXE|1|A|A|41
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3OXE|1|A|G|62 interacts with 3OXE|1|A|A|41
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3OXE|1|A|A|41 B=3OXE|1|A|G|62
  4 Basepair    41   62 AG tHS 
No need to probe because of interaction between a=3OXE|1|A|G|42 B=3OXE|1|A|U|61
  5 Basepair    42   61 GU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3OXE|1|A|A|40
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3OXE|1|A|A|63
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G38 - C66 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: 'AA'
               Comment: ' // Basepair C39 - A64 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3OXE|1|A|A|40'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3OXE|1|A|A|63'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A41 - G62 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G42 - U61 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  10   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_01038.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8083

Timestamp 18-Jul-2025 22:46:27
pMakeSCFGModels: Making JAR3D model for motif group IL_01176.1, number 6 of 411
pMakeNodes starting loop:     a=6FZ0|1|A|C|24 B=6FZ0|1|A|G|43
  2 Basepair    24   43 CG cWW 
pMakeNodes probe for inserts:  a=6FZ0|1|A|G|25 B=6FZ0|1|A|A|42
    Insertion on left  6FZ0|1|A|G|25
pMakeNodesProbeForInsertions:  a 6FZ0|1|A|C|26 interacts with 6FZ0|1|A|A|42
pMakeNodesProbeForInsertions:  B 6FZ0|1|A|A|42 interacts with 6FZ0|1|A|C|26
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6FZ0|1|A|A|42 interacts with 6FZ0|1|A|C|26
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6FZ0|1|A|C|26 B=6FZ0|1|A|A|42
  3 Basepair    26   42 CA cSS 
No need to probe because of interaction between a=6FZ0|1|A|C|27 B=6FZ0|1|A|A|41
  4 Basepair    27   41 CA cSS 
pMakeNodes probe for inserts:  a=6FZ0|1|A|U|28 B=6FZ0|1|A|A|40
    Insertion on left  6FZ0|1|A|U|28
    Insertion on right 6FZ0|1|A|A|40
pMakeNodesProbeForInsertions:  a 6FZ0|1|A|U|29 interacts with 6FZ0|1|A|A|39
pMakeNodesProbeForInsertions:  B 6FZ0|1|A|A|39 interacts with 6FZ0|1|A|U|29
pMakeNodesProbeForInsertions:  B 6FZ0|1|A|A|39 interacts with 6FZ0|1|A|U|29
pMakeNodes probed for insert:  a=6FZ0|1|A|U|29 B=6FZ0|1|A|A|39
  5 Basepair    29   39 UA cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6FZ0|1|A|G|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6FZ0|1|A|U|28
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6FZ0|1|A|A|40
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CG'
           RightLetter: 'G'
               Comment: ' // Basepair C24 - G43 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6FZ0|1|A|G|25'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'CU'
           RightLetter: 'AA'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C26 - A42 cSS '
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CU'
           RightLetter: 'AA'
               Comment: ' // Basepair C27 - A41 cSS '
              NumLoops: []
                  Edge: 11
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6FZ0|1|A|U|28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6FZ0|1|A|A|40'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U29 - A39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  6 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  12   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_01176.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.1223

Timestamp 18-Jul-2025 22:46:28
pMakeSCFGModels: Making JAR3D model for motif group IL_01488.3, number 7 of 411
pMakeNodes starting loop:     a=6UFM|1|B|C|3 B=6UFM|1|B|G|27
pMakeNodes making a cluster near strand break a=6UFM|1|B|C|3 B=6UFM|1|B|G|27
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 10 to 12
aa is 5 bb is 10
  2 Cluster   6UFM|1|B|C|3:6UFM|1|B|A|8 6UFM|1|B|G|25:6UFM|1|B|G|27
    LR Inter  6UFM|1|B|A|8 6UFM|1|B|G|25 tHS 
    LR Inter  6UFM|1|B|G|4 6UFM|1|B|A|26 tSS 
    LR Inter  6UFM|1|B|G|7 6UFM|1|B|A|26 tSH 
    LR Inter  6UFM|1|B|C|3 6UFM|1|B|G|27 cWW 
    LR Inter  6UFM|1|B|A|8 6UFM|1|B|G|27 tSS 
    Left  strand conserved insertion 6UFM|1|B|A|5 at position 3
pMakeNodesCluster a=6 B=9 at the end
pMakeNodesCluster a=6 B=9 at the end
No need to probe because of interaction between a=6UFM|1|B|U|9 B=6UFM|1|B|G|24
  3 Basepair     9   24 UG tHS 
No need to probe because of interaction between a=6UFM|1|B|C|10 B=6UFM|1|B|G|23
  4 Basepair    10   23 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 10 11 12
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 0 0 0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: [10 11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CGAGA'
           RightLetter: 'GAG'
               Comment: ' // Cluster node 6UFM|1|B|C|3:6UFM|1|B|A|8 and 6UFM|1|B|G|25:6UFM|1|B|G|27'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
          LeftNotInter: 3
         RightNotInter: [1×0 double]
              NormCons: 0.0180
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U9 - G24 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C10 - G23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 10 11 12
pMakeMotifModelFromSSF:   3   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_01488.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3878
   -6.8069
   -6.5236
   -9.4613
   -6.7243
   -8.5125
  -12.4954
   -6.8069
  -10.8548
   -6.6577

Timestamp 18-Jul-2025 22:46:29
pMakeSCFGModels: Making JAR3D model for motif group IL_01994.1, number 8 of 411
pMakeNodes starting loop:     a=6DLR|1|A|G|36 B=6DLR|1|A|C|23
  2 Basepair    36   23 GC cWW 
pMakeNodes probe for inserts:  a=6DLR|1|A|G|37 B=6DLR|1|A|G|22
pMakeNodesProbeForInsertions:  a 6DLR|1|A|G|37 interacts with 6DLR|1|A|G|41
pMakeNodesProbeForInsertions:  B 6DLR|1|A|G|22 interacts with 6DLR|1|A|C|39
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6DLR|1|A|G|22 interacts with 6DLR|1|A|U|40
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6DLR|1|A|G|37 B=6DLR|1|A|G|22
pMakeNodes making a cluster near strand break a=6DLR|1|A|G|37 B=6DLR|1|A|G|22
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 5 and then 6 to 7
aa is 5 bb is 6
  3 Cluster   6DLR|1|A|G|37:6DLR|1|A|G|41 6DLR|1|A|C|21:6DLR|1|A|G|22
    LR Inter  6DLR|1|A|G|41 6DLR|1|A|C|21 cWW 
    LR Inter  6DLR|1|A|C|39 6DLR|1|A|G|22 cWW 
    LR Inter  6DLR|1|A|U|40 6DLR|1|A|G|22 tHS 
    LL Inter  6DLR|1|A|C|39 6DLR|1|A|U|40 cSH 
    LL Inter  6DLR|1|A|G|37 6DLR|1|A|G|41 cWH 
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5 Right  6  7
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G36 - C23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5]
            RightIndex: [6 7]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCUG'
           RightLetter: 'CG'
               Comment: ' // Cluster node 6DLR|1|A|G|37:6DLR|1|A|G|41 and 6DLR|1|A|C|21:6DLR|1|A|G|22'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: [1 2]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0041

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5 Right  6  7
pMakeMotifModelFromSSF:   4   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_01994.1 allow insertions from initial node 4?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_01994.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.2234
   -4.2234
   -4.1444

Timestamp 18-Jul-2025 22:46:30
pMakeSCFGModels: Making JAR3D model for motif group IL_02203.1, number 9 of 411
pMakeNodes starting loop:     a=4V9F|1|0|A|965 B=4V9F|1|0|U|1003
  2 Basepair   965 1003 AU cWW 
No need to probe because of interaction between a=4V9F|1|0|U|966 B=4V9F|1|0|G|1002
  3 Basepair   966 1002 UG cSW 
No need to probe because of interaction between a=4V9F|1|0|U|967 B=4V9F|1|0|U|1001
  4 Basepair   967 1001 UU cWW 
No need to probe because of interaction between a=4V9F|1|0|G|968 B=4V9F|1|0|C|1000
  5 Basepair   968 1000 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A965 - U1003 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U966 - G1002 cSW '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U967 - U1001 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G968 - C1000 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_02203.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.4173

Timestamp 18-Jul-2025 22:46:30
pMakeSCFGModels: Making JAR3D model for motif group IL_02349.4, number 10 of 411
pMakeNodes starting loop:     a=4Y1M|1|B|G|8 B=4Y1M|1|B|C|101
  2 Basepair     8  101 GC cWW 
No need to probe because of interaction between a=4Y1M|1|B|G|9 B=4Y1M|1|B|A|100
  3 Basepair     9  100 GA tSH 
No need to probe because of interaction between a=4Y1M|1|B|G|10 B=4Y1M|1|B|G|99
  4 Basepair    10   99 GG tWH 
pMakeNodes probe for inserts:  a=4Y1M|1|B|G|12 B=4Y1M|1|B|A|98
pMakeNodesProbeForInsertions:  a 4Y1M|1|B|G|12 interacts with 4Y1M|1|B|U|13
pMakeNodesProbeForInsertions:  B 4Y1M|1|B|A|98 interacts with 4Y1M|1|B|U|13
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4Y1M|1|B|A|98 interacts with 4Y1M|1|B|U|13
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4Y1M|1|B|G|12 B=4Y1M|1|B|A|98
pMakeNodes making a cluster near strand break a=4Y1M|1|B|G|12 B=4Y1M|1|B|A|98
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 10 to 10
aa is 5 bb is 10
  5 Cluster   4Y1M|1|B|G|12:4Y1M|1|B|U|13 4Y1M|1|B|A|98:4Y1M|1|B|A|98
    LR Inter  4Y1M|1|B|U|13 4Y1M|1|B|A|98 tWH 
    LL Inter  4Y1M|1|B|G|12 4Y1M|1|B|U|13 cSH 
pMakeNodesCluster a=6 B=9 at the end
pMakeNodesCluster a=6 B=9 at the end
No need to probe because of interaction between a=4Y1M|1|B|A|14 B=4Y1M|1|B|G|97
  6 Basepair    14   97 AG tHS 
No need to probe because of interaction between a=4Y1M|1|B|G|15 B=4Y1M|1|B|C|96
  7 Basepair    15   96 GC cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G8 - C101 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G9 - A100 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G10 - G99 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [4 5]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 4Y1M|1|B|G|12:4Y1M|1|B|U|13 and 4Y1M|1|B|A|98:4Y1M|1|B|A|98'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A14 - G97 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G15 - C96 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_02349.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0968
   -6.0968
   -6.3556

Timestamp 18-Jul-2025 22:46:31
pMakeSCFGModels: Making JAR3D model for motif group IL_02555.1, number 11 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|2540 B=5J7L|1|DA|G|2523
  2 Basepair  2540 2523 CG cWW 
No need to probe because of interaction between a=5J7L|1|DA|A|2541 B=5J7L|1|DA|U|2522
pMakeNodes making a cluster near strand break a=5J7L|1|DA|A|2541 B=5J7L|1|DA|U|2522
pMakeNodesCluster: amax is 3 bmin is 4, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 3 and then 4 to 4
aa is 3 bb is 4
  3 Cluster   5J7L|1|DA|A|2541:5J7L|1|DA|G|2543 5J7L|1|DA|U|2522:5J7L|1|DA|U|2522
    LR Inter  5J7L|1|DA|A|2541 5J7L|1|DA|U|2522 tSH 
    LR Inter  5J7L|1|DA|G|2543 5J7L|1|DA|U|2522 cWW 
pMakeNodesCluster a=4 B=3 at the end
pMakeNodesCluster a=4 B=3 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2540 - G2523 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3]
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AG'
           RightLetter: 'U'
               Comment: ' // Cluster node 5J7L|1|DA|A|2541:5J7L|1|DA|G|2543 and 5J7L|1|DA|U|2522:5J7L|1|DA|U|2522'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2741

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  3
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_02555.1 allow insertions from initial node 4?
ans =

    0.9923    0.0074    0.0003


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9923    0.0074    0.0003


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_02555.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.3022
   -2.3022
   -2.3022
   -2.3022
   -2.3022
   -2.5177
   -2.5177
   -5.9675
   -5.9105

Timestamp 18-Jul-2025 22:46:31
pMakeSCFGModels: Making JAR3D model for motif group IL_03109.3, number 12 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|C|443 B=8P9A|1|sR|G|461
pMakeNodes making a cluster near strand break a=8P9A|1|sR|C|443 B=8P9A|1|sR|G|461
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 6 to 7
aa is 5 bb is 6
  2 Cluster   8P9A|1|sR|C|443:8P9A|1|sR|U|447 8P9A|1|sR|A|460:8P9A|1|sR|G|461
    LR Inter  8P9A|1|sR|C|444 8P9A|1|sR|A|460 tWH 
    LR Inter  8P9A|1|sR|U|447 8P9A|1|sR|A|460 cWW 
    LR Inter  8P9A|1|sR|C|443 8P9A|1|sR|G|461 cWW 
    LR Inter  8P9A|1|sR|A|446 8P9A|1|sR|G|461 cWS 
    LL Inter  8P9A|1|sR|C|443 8P9A|1|sR|A|445 cSH 
    LL Inter  8P9A|1|sR|C|444 8P9A|1|sR|A|446 cSH 
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  3 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  6  7
pMakeMotifModelFromSSF:   3   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: [6 7]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCAAU'
           RightLetter: 'AG'
               Comment: ' // Cluster node 8P9A|1|sR|C|443:8P9A|1|sR|U|447 and 8P9A|1|sR|A|460:8P9A|1|sR|G|461'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0016

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  6  7
pMakeMotifModelFromSSF:   3   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 4
pUpdateModelWithSSF: IL_03109.3 allow insertions from initial node 3?
ans =

    0.9912    0.0084    0.0004


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9912    0.0084    0.0004


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_03109.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.4885
   -3.4885
   -3.7523
   -4.5827
   -8.1832
   -6.9320

Timestamp 18-Jul-2025 22:46:32
pMakeSCFGModels: Making JAR3D model for motif group IL_03350.1, number 13 of 411
pMakeNodes starting loop:     a=4PHY|1|A|C|5 B=4PHY|1|B|G|41
  2 Basepair     5   41 CG cWW 
pMakeNodes probe for inserts:  a=4PHY|1|A|U|6 B=4PHY|1|B|G|40
pMakeNodesProbeForInsertions:  a 4PHY|1|A|U|6 interacts with 4PHY|1|B|A|39
pMakeNodesProbeForInsertions:  B 4PHY|1|B|G|40 interacts with 4PHY|1|A|C|12
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4PHY|1|B|G|40 interacts with 4PHY|1|A|C|12
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4PHY|1|A|U|6 B=4PHY|1|B|G|40
pMakeNodes making a cluster near strand break a=4PHY|1|A|U|6 B=4PHY|1|B|G|40
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 8 and then 11 to 12
aa is 8 bb is 11
  3 Cluster   4PHY|1|A|U|6:4PHY|1|A|C|12 4PHY|1|B|A|39:4PHY|1|B|G|40
    LR Inter  4PHY|1|A|U|6 4PHY|1|B|A|39 tWH 
    LR Inter  4PHY|1|A|C|12 4PHY|1|B|G|40 cWW 
    Left  strand conserved insertion 4PHY|1|A|C|7 at position 2
    Left  strand conserved insertion 4PHY|1|A|C|8 at position 3
    Left  strand conserved insertion 4PHY|1|A|C|9 at position 4
    Left  strand conserved insertion 4PHY|1|A|C|10 at position 5
    Left  strand conserved insertion 4PHY|1|A|A|11 at position 6
pMakeNodesCluster a=9 B=10 at the end
pMakeNodesCluster a=9 B=10 at the end
No need to probe because of interaction between a=4PHY|1|A|C|13 B=4PHY|1|B|G|38
  4 Basepair    13   38 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8 Right 11 12
pMakeMotifModelFromSSF:   4  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   5   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C5 - G41 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5 6 7 8]
            RightIndex: [11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UCCCCAC'
           RightLetter: 'AG'
               Comment: ' // Cluster node 4PHY|1|A|U|6:4PHY|1|A|C|12 and 4PHY|1|B|A|39:4PHY|1|B|G|40'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7]
                 Right: [1 2]
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4 5 6]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C13 - G38 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8 Right 11 12
pMakeMotifModelFromSSF:   4   Initial Left  9 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   6   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_03350.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8058
   -7.2950
   -7.2950

Timestamp 18-Jul-2025 22:46:32
pMakeSCFGModels: Making JAR3D model for motif group IL_04021.2, number 14 of 411
pMakeNodes starting loop:     a=4WF9|1|X|G|24 B=4WF9|1|X|C|561
  2 Basepair    24  561 GC cWW 
pMakeNodes probe for inserts:  a=4WF9|1|X|U|25 B=4WF9|1|X|A|560
    Insertion on left  4WF9|1|X|U|25
    Insertion on right 4WF9|1|X|A|560
pMakeNodesProbeForInsertions:  a 4WF9|1|X|G|26 interacts with 4WF9|1|X|A|559
pMakeNodesProbeForInsertions:  B 4WF9|1|X|A|559 interacts with 4WF9|1|X|G|26
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4WF9|1|X|A|559 interacts with 4WF9|1|X|G|26
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4WF9|1|X|G|26 B=4WF9|1|X|A|559
  3 Basepair    26  559 GA tSH 
No need to probe because of interaction between a=4WF9|1|X|G|27 B=4WF9|1|X|A|558
  4 Basepair    27  558 GA tSH 
No need to probe because of interaction between a=4WF9|1|X|A|28 B=4WF9|1|X|G|557
  5 Basepair    28  557 AG tHS 
No need to probe because of interaction between a=4WF9|1|X|U|29 B=4WF9|1|X|U|556
  6 Basepair    29  556 UU cWW 
No need to probe because of interaction between a=4WF9|1|X|G|30 B=4WF9|1|X|C|555
  7 Basepair    30  555 GC cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right 11
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|U|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WF9|1|X|A|560
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GU'
           RightLetter: 'AC'
               Comment: ' // Basepair G24 - C561 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|U|25'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WF9|1|X|A|560'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G26 - A559 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G27 - A558 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A28 - G557 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U29 - U556 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G30 - C555 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 13
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 13
pMakeMotifModelFromSSF:   6   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right 11
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  12   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_04021.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1612
   -6.1612
   -6.1612
   -7.5347
   -6.1612
   -7.5347
   -7.3402

Timestamp 18-Jul-2025 22:46:33
pMakeSCFGModels: Making JAR3D model for motif group IL_04073.1, number 15 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|A|1209 B=8CRE|1|CM|U|1244
  2 Basepair  1209 1244 AU cWW 
pMakeNodes probe for inserts:  a=8CRE|1|CM|U|1210 B=8CRE|1|CM|U|1242
    Insertion on left  8CRE|1|CM|U|1210
    Insertion on right 8CRE|1|CM|U|1242
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|A|1211 interacts with 8CRE|1|CM|A|1241
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|A|1241 interacts with 8CRE|1|CM|A|1211
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|A|1241 interacts with 8CRE|1|CM|G|1214
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8CRE|1|CM|A|1211 B=8CRE|1|CM|A|1241
pMakeNodes making a cluster near strand break a=8CRE|1|CM|A|1211 B=8CRE|1|CM|A|1241
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 5 and then 16 to 16
aa is 5 bb is 16
  3 Cluster   8CRE|1|CM|A|1211:8CRE|1|CM|G|1214 8CRE|1|CM|A|1241:8CRE|1|CM|A|1241
    LR Inter  8CRE|1|CM|A|1211 8CRE|1|CM|A|1241 tSS 
    LR Inter  8CRE|1|CM|G|1214 8CRE|1|CM|A|1241 tSH 
    Left  strand conserved insertion 8CRE|1|CM|A|1212 at position 2
pMakeNodesCluster a=6 B=15 at the end
pMakeNodesCluster a=6 B=15 at the end
No need to probe because of interaction between a=8CRE|1|CM|A|1215 B=8CRE|1|CM|G|1240
  4 Basepair  1215 1240 AG tHS 
No need to probe because of interaction between a=8CRE|1|CM|U|1216 B=8CRE|1|CM|U|1239
  5 Basepair  1216 1239 UU cWW 
No need to probe because of interaction between a=8CRE|1|CM|U|1217 B=8CRE|1|CM|U|1238
  6 Basepair  1217 1238 UU cWW 
pMakeNodes probe for inserts:  a=8CRE|1|CM|G|1218 B=8CRE|1|CM|C|1237
    Insertion on left  8CRE|1|CM|G|1218
    Insertion on right 8CRE|1|CM|C|1237
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|A|1219 interacts with 8CRE|1|CM|U|1236
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|U|1236 interacts with 8CRE|1|CM|A|1219
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|U|1236 interacts with 8CRE|1|CM|A|1219
pMakeNodes probed for insert:  a=8CRE|1|CM|A|1219 B=8CRE|1|CM|U|1236
  7 Basepair  1219 1236 AU cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3   Cluster Left  3  4  5 Right 16
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right 15
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right 14
pMakeMotifModelFromSSF:   6  Basepair Left  8 Right 13
pMakeMotifModelFromSSF:   7  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   8   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|U|1210
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|CM|A|1241
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|U|1217
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|CM|U|1236
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AU'
           RightLetter: 'UU'
               Comment: ' // Basepair A1209 - U1244 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|U|1210'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2278

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|CM|A|1241'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [3 4 5]
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAG'
           RightLetter: 'A'
               Comment: ' // Cluster node 8CRE|1|CM|A|1211:8CRE|1|CM|G|1214 and 8CRE|1|CM|A|1241:8CRE|1|CM|A|1241'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2278

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1215 - G1240 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U1216 - U1239 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UG'
           RightLetter: 'CU'
               Comment: ' // Basepair U1217 - U1238 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|U|1217'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 10
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 10
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|CM|U|1236'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 17
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A1219 - U1236 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 20
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 17
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 17
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 17
pMakeMotifModelFromSSF:   6   Initial Left  3 Right 16
pMakeMotifModelFromSSF:   7   Cluster Left  3  4  5 Right 16
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 15
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right 15
pMakeMotifModelFromSSF:  10  Basepair Left  7 Right 14
pMakeMotifModelFromSSF:  11  Basepair Left  8 Right 13
pMakeMotifModelFromSSF:  12     Fixed Left  9 Right 12
pMakeMotifModelFromSSF:  13   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  14     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  15   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  16  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  17   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a hairpin at node 17

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_04073.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.2606

Timestamp 18-Jul-2025 22:46:33
pMakeSCFGModels: Making JAR3D model for motif group IL_04307.1, number 16 of 411
pMakeNodes starting loop:     a=7VYX|1|C|C|41 B=7VYX|1|C|G|21
  2 Basepair    41   21 CG cWW 
No need to probe because of interaction between a=7VYX|1|C|C|42 B=7VYX|1|C|A|20
  3 Basepair    42   20 CA cWW 
pMakeNodes probe for inserts:  a=7VYX|1|C|A|43 B=7VYX|1|C|C|19
    Insertion on left  7VYX|1|C|A|43
    Insertion on left  7VYX|1|C|U|44
    Insertion on left  7VYX|1|C|A|45
    Insertion on left  7VYX|1|C|C|46
    Insertion on left  7VYX|1|C|C|47
    Insertion on left  7VYX|1|C|U|48
    Insertion on left  7VYX|1|C|U|49
    Insertion on right 7VYX|1|C|C|19
    Insertion on right 7VYX|1|C|U|18
    Insertion on right 7VYX|1|C|C|17
pMakeNodesProbeForInsertions:  a 7VYX|1|C|G|50 interacts with 7VYX|1|C|C|16
pMakeNodesProbeForInsertions:  B 7VYX|1|C|C|16 interacts with 7VYX|1|C|G|50
pMakeNodesProbeForInsertions:  B 7VYX|1|C|C|16 interacts with 7VYX|1|C|G|50
pMakeNodes probed for insert:  a=7VYX|1|C|G|50 B=7VYX|1|C|C|16
  4 Basepair    50   16 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 15
pMakeMotifModelFromSSF:   4  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   5   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7VYX|1|C|U|18
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7VYX|1|C|C|19
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7VYX|1|C|A|20
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7VYX|1|C|G|21
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7VYX|1|C|C|41
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7VYX|1|C|C|42
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7VYX|1|C|A|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7VYX|1|C|U|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7VYX|1|C|C|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7VYX|1|C|C|46
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C41 - G21 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAUACCUU'
           RightLetter: 'CUCA'
               Comment: ' // Basepair C42 - A20 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7VYX|1|C|U|18'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7VYX|1|C|C|19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7VYX|1|C|A|20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7VYX|1|C|G|21'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7VYX|1|C|C|41'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7VYX|1|C|C|42'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7VYX|1|C|A|43'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 10
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7VYX|1|C|U|48'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7VYX|1|C|C|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             LeftIndex: 10
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 23
             LeftIndex: 10
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7VYX|1|C|C|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 25
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G50 - C16 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 27
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 15
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 14
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 14
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 14
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 14
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 14
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 14
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 14
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 14
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 14
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 14
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 14
pMakeMotifModelFromSSF:  16     Fixed Left  9 Right 14
pMakeMotifModelFromSSF:  17   Initial Left 10 Right 14
pMakeMotifModelFromSSF:  18     Fixed Left 10 Right 14
pMakeMotifModelFromSSF:  19   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  20     Fixed Left 10 Right 13
pMakeMotifModelFromSSF:  21   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  22     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  23   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  24  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  25   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Found a hairpin at node 25

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_04307.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.2277

Timestamp 18-Jul-2025 22:46:34
pMakeSCFGModels: Making JAR3D model for motif group IL_04332.3, number 17 of 411
pMakeNodes starting loop:     a=7A0S|1|X|C|1917 B=7A0S|1|X|G|1947
  2 Basepair  1917 1947 CG cWW 
pMakeNodes probe for inserts:  a=7A0S|1|X|G|1918 B=7A0S|1|X|C|1945
    Insertion on left  7A0S|1|X|G|1918
    Insertion on right 7A0S|1|X|C|1945
pMakeNodesProbeForInsertions:  a 7A0S|1|X|A|1919 interacts with 7A0S|1|X|U|1926
pMakeNodesProbeForInsertions:  B 7A0S|1|X|C|1944 interacts with 7A0S|1|X|G|1928
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 7A0S|1|X|C|1944 interacts with 7A0S|1|X|G|1928
pMakeNodes probed for insert:  a=7A0S|1|X|A|1919 B=7A0S|1|X|C|1944
pMakeNodes making a cluster near strand break a=7A0S|1|X|A|1919 B=7A0S|1|X|C|1944
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 10 and then 11 to 11
aa is 10 bb is 11
  3 Cluster   7A0S|1|X|A|1919:7A0S|1|X|G|1928 7A0S|1|X|C|1944:7A0S|1|X|C|1944
    LR Inter  7A0S|1|X|G|1928 7A0S|1|X|C|1944 cWW 
    LL Inter  7A0S|1|X|U|1923 7A0S|1|X|C|1925 tSW 
    LL Inter  7A0S|1|X|A|1919 7A0S|1|X|U|1926 cWW 
    Left  strand conserved insertion 7A0S|1|X|A|1920 at position 2
    Left  strand conserved insertion 7A0S|1|X|U|1922 at position 3
    Left  strand conserved insertion 7A0S|1|X|C|1924 at position 5
pMakeNodesCluster a=11 B=10 at the end
pMakeNodesCluster a=11 B=10 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  3  4  5  6  7  8  9 10 Right 11
pMakeMotifModelFromSSF:   4   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|G|1918
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|G|1928
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CG'
           RightLetter: 'CG'
               Comment: ' // Basepair C1917 - G1947 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7A0S|1|X|G|1918'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 5]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7A0S|1|X|G|1928'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [3 4 5 6 7 8 9 10]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAUUCCUG'
           RightLetter: 'C'
               Comment: ' // Cluster node 7A0S|1|X|A|1919:7A0S|1|X|G|1928 and 7A0S|1|X|C|1944:7A0S|1|X|C|1944'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 5]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   7   Cluster Left  3  4  5  6  7  8  9 10 Right 11
pMakeMotifModelFromSSF:   8   Initial Left 11 Right 10
pMakeMotifModelFromSSF:   9   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 9
pUpdateModelWithSSF: IL_04332.3 allow insertions from initial node 8?
ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_04332.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.3727
   -8.7788

Timestamp 18-Jul-2025 22:46:34
pMakeSCFGModels: Making JAR3D model for motif group IL_04346.10, number 18 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|C|201 B=9DFE|1|1A|G|194
  2 Basepair   201  194 CG cWW 
No need to probe because of interaction between a=9DFE|1|1A|U|202 B=9DFE|1|1A|U|193
  3 Basepair   202  193 UU cWW 
No need to probe because of interaction between a=9DFE|1|1A|C|203 B=9DFE|1|1A|C|192
  4 Basepair   203  192 CC tSH 
No need to probe because of interaction between a=9DFE|1|1A|A|204 B=9DFE|1|1A|A|191
  5 Basepair   204  191 AA tHH 
pMakeNodes probe for inserts:  a=9DFE|1|1A|G|205 B=9DFE|1|1A|A|190
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|G|205 interacts with 9DFE|1|1A|U|206
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|A|190 interacts with 9DFE|1|1A|U|206
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|A|190 interacts with 9DFE|1|1A|U|206
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=9DFE|1|1A|G|205 B=9DFE|1|1A|A|190
pMakeNodes making a cluster near strand break a=9DFE|1|1A|G|205 B=9DFE|1|1A|A|190
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 6 and then 11 to 11
aa is 6 bb is 11
  6 Cluster   9DFE|1|1A|G|205:9DFE|1|1A|U|206 9DFE|1|1A|A|190:9DFE|1|1A|A|190
    LR Inter  9DFE|1|1A|U|206 9DFE|1|1A|A|190 tWH 
    LL Inter  9DFE|1|1A|G|205 9DFE|1|1A|U|206 cSH 
pMakeNodesCluster a=7 B=10 at the end
pMakeNodesCluster a=7 B=10 at the end
No need to probe because of interaction between a=9DFE|1|1A|A|207 B=9DFE|1|1A|G|189
  7 Basepair   207  189 AG tHS 
No need to probe because of interaction between a=9DFE|1|1A|C|208 B=9DFE|1|1A|G|188
  8 Basepair   208  188 CG cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 12
pMakeMotifModelFromSSF:   6   Cluster Left  5  6 Right 11
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   9   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C201 - G194 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U202 - U193 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C203 - C192 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A204 - A191 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 7
             LeftIndex: [5 6]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 9DFE|1|1A|G|205:9DFE|1|1A|U|206 and 9DFE|1|1A|A|190:9DFE|1|1A|A|190'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A207 - G189 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C208 - G188 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 12
pMakeMotifModelFromSSF:   6   Cluster Left  5  6 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_04346.10_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.9350
   -8.2148
   -8.1689
   -7.9350
   -9.4156
   -9.7918
   -9.6575
  -11.3924
  -11.3924
  -10.2946
   -8.0879
   -8.6031
   -8.0879
   -9.4688
   -9.5162

Timestamp 18-Jul-2025 22:46:36
pMakeSCFGModels: Making JAR3D model for motif group IL_04600.1, number 19 of 411
pMakeNodes starting loop:     a=5XWG|1|A|5BU|9||||14_445 B=5XWG|1|A|A|15
  2 Basepair     9   15 UA cWW 
No need to probe because of interaction between a=5XWG|1|A|C|10||||14_445 B=5XWG|1|A|A|14
  3 Basepair    10   14 CA cWW 
No need to probe because of interaction between a=5XWG|1|A|G|11||||14_445 B=5XWG|1|A|A|13
  4 Basepair    11   13 GA tSH 
pMakeNodes probe for inserts:  a=5XWG|1|A|A|12||||14_445 B=5XWG|1|A|A|12
    Insertion on left  5XWG|1|A|A|12||||14_445
    Insertion on right 5XWG|1|A|A|12
pMakeNodesProbeForInsertions:  a 5XWG|1|A|A|13||||14_445 interacts with 5XWG|1|A|G|11
pMakeNodesProbeForInsertions:  B 5XWG|1|A|G|11 interacts with 5XWG|1|A|A|13||||14_445
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5XWG|1|A|G|11 interacts with 5XWG|1|A|A|13||||14_445
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5XWG|1|A|A|13||||14_445 B=5XWG|1|A|G|11
  5 Basepair    13   11 AG tHS 
No need to probe because of interaction between a=5XWG|1|A|A|14||||14_445 B=5XWG|1|A|C|10
  6 Basepair    14   10 AC cWW 
No need to probe because of interaction between a=5XWG|1|A|A|15||||14_445 B=5XWG|1|A|5BU|9
  7 Basepair    15    9 AU cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5XWG|1|A|A|12||||14_445
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5XWG|1|A|A|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U9 - A15 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C10 - A14 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'AA'
               Comment: ' // Basepair G11 - A13 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5XWG|1|A|A|12||||14_445'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5XWG|1|A|A|12'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A13 - G11 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A14 - C10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A15 - U9 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  12   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_04600.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.6710

Timestamp 18-Jul-2025 22:46:36
pMakeSCFGModels: Making JAR3D model for motif group IL_04638.3, number 20 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|C|2774 B=9DFE|1|1A|G|2640
  2 Basepair  2774 2640 CG cWW 
No need to probe because of interaction between a=9DFE|1|1A|A|2775 B=9DFE|1|1A|A|2639
  3 Basepair  2775 2639 AA tSH 
pMakeNodes probe for inserts:  a=9DFE|1|1A|A|2776 B=9DFE|1|1A|G|2638
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|A|2776 interacts with 9DFE|1|1A|U|2637
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|G|2638 interacts with 9DFE|1|1A|A|2778
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|G|2638 interacts with 9DFE|1|1A|A|2778
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=9DFE|1|1A|A|2776 B=9DFE|1|1A|G|2638
pMakeNodes making a cluster near strand break a=9DFE|1|1A|A|2776 B=9DFE|1|1A|G|2638
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 6 and then 10 to 11
aa is 6 bb is 10
  4 Cluster   9DFE|1|1A|A|2776:9DFE|1|1A|U|2779 9DFE|1|1A|U|2637:9DFE|1|1A|G|2638
    LR Inter  9DFE|1|1A|A|2776 9DFE|1|1A|U|2637 tHW 
    LR Inter  9DFE|1|1A|A|2778 9DFE|1|1A|G|2638 tHS 
    LL Inter  9DFE|1|1A|G|2777 9DFE|1|1A|U|2779 cSH 
pMakeNodesCluster a=7 B=9 at the end
pMakeNodesCluster a=7 B=9 at the end
pMakeNodes probe for inserts:  a=9DFE|1|1A|A|2781 B=9DFE|1|1A|U|2636
    Insertion on left  9DFE|1|1A|A|2781
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|G|2782 interacts with 9DFE|1|1A|U|2636
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|U|2636 interacts with 9DFE|1|1A|G|2782
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|U|2636 interacts with 9DFE|1|1A|G|2782
  5 Initial   2781 (1 insertion) and 2636 (0 insertion)
pMakeNodes probed for insert:  a=9DFE|1|1A|G|2782 B=9DFE|1|1A|U|2636
  6 Basepair  2782 2636 GU cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6 Right 10 11
pMakeMotifModelFromSSF:   5   Initial Left  7 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   7   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|A|2775
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2774 - G2640 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A2775 - A2639 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4 5 6]
            RightIndex: [10 11]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGAU'
           RightLetter: 'UG'
               Comment: ' // Cluster node 9DFE|1|1A|A|2776:9DFE|1|1A|U|2779 and 9DFE|1|1A|U|2637:9DFE|1|1A|G|2638'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: [1 2]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 9DFE|1|1A|A|2781 - 9DFE|1|1A|U|2636 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|A|2775'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G2782 - U2636 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6 Right 10 11
pMakeMotifModelFromSSF:   5   Initial Left  7 Right  9
pMakeMotifModelFromSSF:   6     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:   7   Initial Left  8 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   9   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_04638.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.8971
   -8.8971
   -8.8971
   -9.6108
   -9.9504

Timestamp 18-Jul-2025 22:46:37
pMakeSCFGModels: Making JAR3D model for motif group IL_04650.2, number 21 of 411
pMakeNodes starting loop:     a=6TFF|1|A|A|7 B=6TFF|1|A|U|46
pMakeNodes making a cluster near strand break a=6TFF|1|A|A|7 B=6TFF|1|A|U|46
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 11 to 11
aa is 2 bb is 11
  2 Cluster   6TFF|1|A|A|7:6TFF|1|A|A|8 6TFF|1|A|U|46:6TFF|1|A|U|46
    LR Inter  6TFF|1|A|A|7 6TFF|1|A|U|46 cWW 
    LL Inter  6TFF|1|A|A|7 6TFF|1|A|A|8 cSH 
pMakeNodesCluster a=3 B=10 at the end
pMakeNodesCluster a=3 B=10 at the end
pMakeNodes probe for inserts:  a=6TFF|1|A|C|9 B=6TFF|1|A|C|45
    Insertion on left  6TFF|1|A|C|9
    Insertion on left  6TFF|1|A|A|10
    Insertion on left  6TFF|1|A|C|12
    Insertion on left  6TFF|1|A|C|13
    Insertion on left  6TFF|1|A|C|14
    Insertion on left  6TFF|1|A|C|15
pMakeNodesProbeForInsertions:  a 6TFF|1|A|G|16 interacts with 6TFF|1|A|C|45
pMakeNodesProbeForInsertions:  B 6TFF|1|A|C|45 interacts with 6TFF|1|A|G|16
pMakeNodesProbeForInsertions:  B 6TFF|1|A|C|45 interacts with 6TFF|1|A|G|16
  3 Initial      9 (6 insertion) and   45 (0 insertion)
pMakeNodes probed for insert:  a=6TFF|1|A|G|16 B=6TFF|1|A|C|45
  4 Basepair    16   45 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 11
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   5   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6TFF|1|A|C|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6TFF|1|A|A|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6TFF|1|A|A|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6TFF|1|A|C|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6TFF|1|A|C|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6TFF|1|A|C|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 0 0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AA'
           RightLetter: 'U'
               Comment: ' // Cluster node 6TFF|1|A|A|7:6TFF|1|A|A|8 and 6TFF|1|A|U|46:6TFF|1|A|U|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2494
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CACCCC'
           RightLetter: []
               Comment: ' // Initial node 6TFF|1|A|C|9 - 6TFF|1|A|C|45 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6TFF|1|A|C|9'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6TFF|1|A|A|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6TFF|1|A|A|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6TFF|1|A|C|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6TFF|1|A|C|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6TFF|1|A|C|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G16 - C45 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 18
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 11
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  16  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  17   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a hairpin at node 17

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_04650.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.4994
   -5.4994
   -5.4994
   -5.4994

Timestamp 18-Jul-2025 22:46:37
pMakeSCFGModels: Making JAR3D model for motif group IL_04736.1, number 22 of 411
pMakeNodes starting loop:     a=3SIV|1|C|C|40 B=3SIV|1|F|G|46
  2 Basepair    40   46 CG cWW 
No need to probe because of interaction between a=3SIV|1|C|G|41 B=3SIV|1|F|U|44
  3 Basepair    41   44 GU tSW 
pMakeNodes probe for inserts:  a=3SIV|1|C|C|42 B=3SIV|1|F|A|43
    Insertion on left  3SIV|1|C|C|42
    Insertion on left  3SIV|1|C|A|43
    Insertion on right 3SIV|1|F|A|43
    Insertion on right 3SIV|1|F|C|42
pMakeNodesProbeForInsertions:  a 3SIV|1|C|U|44 interacts with 3SIV|1|F|G|41
pMakeNodesProbeForInsertions:  B 3SIV|1|F|G|41 interacts with 3SIV|1|C|U|44
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3SIV|1|F|G|41 interacts with 3SIV|1|C|U|44
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3SIV|1|C|U|44 B=3SIV|1|F|G|41
  4 Basepair    44   41 UG tWS 
No need to probe because of interaction between a=3SIV|1|C|G|46 B=3SIV|1|F|C|40
  5 Basepair    46   40 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3SIV|1|C|C|42
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3SIV|1|C|A|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3SIV|1|F|C|42
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3SIV|1|F|G|41
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C40 - G46 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GCA'
           RightLetter: 'CAU'
               Comment: ' // Basepair G41 - U44 tSW '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3SIV|1|C|C|42'
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3SIV|1|C|A|43'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3SIV|1|F|C|42'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3SIV|1|F|G|41'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U44 - G41 tWS '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G46 - C40 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  9
pMakeMotifModelFromSSF:  10     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  11   Initial Left  5 Right  8
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_04736.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3327

Timestamp 18-Jul-2025 22:46:38
pMakeSCFGModels: Making JAR3D model for motif group IL_04785.1, number 23 of 411
pMakeNodes starting loop:     a=6DLR|1|A|G|77 B=6DLR|1|A|C|96
  2 Basepair    77   96 GC cWW 
No need to probe because of interaction between a=6DLR|1|A|G|78 B=6DLR|1|A|G|95
  3 Basepair    78   95 GG bif 
No need to probe because of interaction between a=6DLR|1|A|A|79 B=6DLR|1|A|A|93
  4 Basepair    79   93 AA tWW 
No need to probe because of interaction between a=6DLR|1|A|G|80 B=6DLR|1|A|C|92
  5 Basepair    80   92 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G77 - C96 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G78 - G95 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A79 - A93 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G80 - C92 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_04785.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7283
   -8.1833

Timestamp 18-Jul-2025 22:46:38
pMakeSCFGModels: Making JAR3D model for motif group IL_05192.4, number 24 of 411
pMakeNodes starting loop:     a=3CUL|1|C|U|44 B=3CUL|1|C|G|25
  2 Basepair    44   25 UG cWW 
pMakeNodes probe for inserts:  a=3CUL|1|C|A|45 B=3CUL|1|C|G|24
    Insertion on left  3CUL|1|C|A|45
    Insertion on left  3CUL|1|C|U|46
    Insertion on left  3CUL|1|C|U|47
    Insertion on left  3CUL|1|C|G|48
    Insertion on right 3CUL|1|C|G|24
    Insertion on right 3CUL|1|C|A|23
pMakeNodesProbeForInsertions:  a 3CUL|1|C|G|49 interacts with 3CUL|1|C|C|22
pMakeNodesProbeForInsertions:  B 3CUL|1|C|C|22 interacts with 3CUL|1|C|G|49
pMakeNodesProbeForInsertions:  B 3CUL|1|C|C|22 interacts with 3CUL|1|C|G|49
pMakeNodes probed for insert:  a=3CUL|1|C|G|49 B=3CUL|1|C|C|22
  3 Basepair    49   22 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3CUL|1|C|A|23
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3CUL|1|C|G|24
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3CUL|1|C|G|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3CUL|1|C|U|44
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3CUL|1|C|G|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3CUL|1|C|U|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UAUUG'
           RightLetter: 'AGG'
               Comment: ' // Basepair U44 - G25 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3CUL|1|C|A|23'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3CUL|1|C|G|24'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3CUL|1|C|G|25'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3CUL|1|C|U|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3CUL|1|C|G|48'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3CUL|1|C|U|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G49 - C22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 18
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  9
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  13     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  14   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  15  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  16   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a hairpin at node 16

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_05192.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.7242
   -9.0595
   -9.0486

Timestamp 18-Jul-2025 22:46:38
pMakeSCFGModels: Making JAR3D model for motif group IL_05472.1, number 25 of 411
pMakeNodes starting loop:     a=7JNH|1|B|G|24 B=7JNH|1|B|C|64
  2 Basepair    24   64 GC cWW 
pMakeNodes probe for inserts:  a=7JNH|1|B|U|25 B=7JNH|1|B|U|63
    Insertion on left  7JNH|1|B|U|25
    Insertion on left  7JNH|1|B|U|26
    Insertion on left  7JNH|1|B|U|27
    Insertion on left  7JNH|1|B|U|28
    Insertion on left  7JNH|1|B|U|29
    Insertion on right 7JNH|1|B|U|63
    Insertion on right 7JNH|1|B|U|62
    Insertion on right 7JNH|1|B|U|61
    Insertion on right 7JNH|1|B|U|60
pMakeNodesProbeForInsertions:  a 7JNH|1|B|A|30 interacts with 7JNH|1|B|G|33
pMakeNodesProbeForInsertions:  B 7JNH|1|B|C|59 interacts with 7JNH|1|B|G|33
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 7JNH|1|B|C|59 interacts with 7JNH|1|B|G|33
pMakeNodes probed for insert:  a=7JNH|1|B|A|30 B=7JNH|1|B|C|59
pMakeNodes making a cluster near strand break a=7JNH|1|B|A|30 B=7JNH|1|B|C|59
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 7 to 8 and then 9 to 9
aa is 8 bb is 9
  3 Cluster   7JNH|1|B|A|30:7JNH|1|B|G|33 7JNH|1|B|C|59:7JNH|1|B|C|59
    LR Inter  7JNH|1|B|G|33 7JNH|1|B|C|59 cWW 
    LL Inter  7JNH|1|B|A|30 7JNH|1|B|G|33 cSH 
pMakeNodesCluster a=9 B=8 at the end
pMakeNodesCluster a=9 B=8 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3   Cluster Left  7  8 Right  9
pMakeMotifModelFromSSF:   4   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JNH|1|B|U|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JNH|1|B|U|26
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JNH|1|B|U|27
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JNH|1|B|U|28
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JNH|1|B|U|29
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7JNH|1|B|U|61
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7JNH|1|B|U|60
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7JNH|1|B|C|59
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7JNH|1|B|G|33
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUUUUU'
           RightLetter: 'UUUUC'
               Comment: ' // Basepair G24 - C64 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JNH|1|B|U|25'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2520

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JNH|1|B|U|26'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JNH|1|B|U|27'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JNH|1|B|U|28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JNH|1|B|U|29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7JNH|1|B|U|61'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7JNH|1|B|U|60'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7JNH|1|B|C|59'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7JNH|1|B|G|33'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 22
             LeftIndex: [7 8]
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AG'
           RightLetter: 'C'
               Comment: ' // Cluster node 7JNH|1|B|A|30:7JNH|1|B|G|33 and 7JNH|1|B|C|59:7JNH|1|B|C|59'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2520

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 25
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 13
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 13
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 13
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 13
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 13
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 13
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 13
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 13
pMakeMotifModelFromSSF:  14   Initial Left  7 Right 12
pMakeMotifModelFromSSF:  15     Fixed Left  7 Right 12
pMakeMotifModelFromSSF:  16   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  17     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:  18   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  19     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  20   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  21   Cluster Left  7  8 Right  9
pMakeMotifModelFromSSF:  22   Initial Left  9 Right  8
pMakeMotifModelFromSSF:  23   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 23
pUpdateModelWithSSF: IL_05472.1 allow insertions from initial node 22?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 23

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_05472.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.6565

Timestamp 18-Jul-2025 22:46:39
pMakeSCFGModels: Making JAR3D model for motif group IL_06029.1, number 26 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|2160 B=5J7L|1|DA|G|2128
  2 Basepair  2160 2128 CG cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|C|2161 B=5J7L|1|DA|G|2125
    Insertion on left  5J7L|1|DA|C|2161
    Insertion on left  5J7L|1|DA|G|2162
    Insertion on left  5J7L|1|DA|C|2164
    Insertion on left  5J7L|1|DA|U|2166
    Insertion on left  5J7L|1|DA|U|2167
    Insertion on left  5J7L|1|DA|G|2168
    Insertion on left  5J7L|1|DA|A|2169
    Insertion on left  5J7L|1|DA|A|2170
    Insertion on left  5J7L|1|DA|A|2171
    Insertion on left  5J7L|1|DA|A|2173
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|C|2174 interacts with 5J7L|1|DA|G|2125
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|2125 interacts with 5J7L|1|DA|C|2174
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|2125 interacts with 5J7L|1|DA|C|2174
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5J7L|1|DA|C|2174 B=5J7L|1|DA|G|2125
  3 Basepair  2174 2125 CG cWS 
pMakeNodes probe for inserts:  a=5J7L|1|DA|C|2175 B=5J7L|1|DA|G|2124
    Insertion on right 5J7L|1|DA|G|2124
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|C|2175 interacts with 5J7L|1|DA|G|2123
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|2123 interacts with 5J7L|1|DA|C|2175
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|2123 interacts with 5J7L|1|DA|C|2175
pMakeNodes probed for insert:  a=5J7L|1|DA|C|2175 B=5J7L|1|DA|G|2123
  4 Basepair  2175 2123 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left 12 Right 16
pMakeMotifModelFromSSF:   4  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:   5   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2124
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2125
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|2126
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2127
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2128
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|2160
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|2161
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2162
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|2163
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|2164
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|G|2168
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [17×17 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-11 8.1893e-10 8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 … ]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CCGCUUGAAAA'
           RightLetter: 'G'
               Comment: ' // Basepair C2160 - G2128 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|2124'
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 14
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|2125'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 14
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|2126'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|2127'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|2128'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|2160'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|2161'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|2162'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|2163'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 11
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             LeftIndex: 11
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|2164'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 12
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 24
             LeftIndex: 12
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'GG'
               Comment: ' // Basepair C2174 - G2125 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 25
             LeftIndex: 13
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|G|2168'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 26
             LeftIndex: 13
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 27
             LeftIndex: 13
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2175 - G2123 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 30
             LeftIndex: 14
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 14
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 16
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 16
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 16
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 16
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 16
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 16
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 16
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 16
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 16
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 16
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 16
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 16
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 16
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 16
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 16
pMakeMotifModelFromSSF:  18   Initial Left 10 Right 16
pMakeMotifModelFromSSF:  19     Fixed Left 10 Right 16
pMakeMotifModelFromSSF:  20   Initial Left 11 Right 16
pMakeMotifModelFromSSF:  21     Fixed Left 11 Right 16
pMakeMotifModelFromSSF:  22   Initial Left 12 Right 16
pMakeMotifModelFromSSF:  23  Basepair Left 12 Right 16
pMakeMotifModelFromSSF:  24     Fixed Left 13 Right 15
pMakeMotifModelFromSSF:  25   Initial Left 13 Right 14
pMakeMotifModelFromSSF:  26  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  27   Hairpin Left 14 Right 13
pNextNodeJunction: Found a hairpin at node 27
pNextNodeJunction: Found a hairpin at node 27

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_06029.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -15.4384

Timestamp 18-Jul-2025 22:46:39
pMakeSCFGModels: Making JAR3D model for motif group IL_06136.2, number 27 of 411
pMakeNodes starting loop:     a=3FTF|1|C|G|1515 B=3FTF|1|D|C|1520
  2 Basepair  1515 1520 GC cWW 
No need to probe because of interaction between a=3FTF|1|C|G|1516 B=3FTF|1|D|A|1519
  3 Basepair  1516 1519 GA tSH 
No need to probe because of interaction between a=3FTF|1|C|G|1517 B=3FTF|1|D|A|1518
  4 Basepair  1517 1518 GA tSH 
No need to probe because of interaction between a=3FTF|1|C|A|1518 B=3FTF|1|D|G|1517
  5 Basepair  1518 1517 AG tHS 
No need to probe because of interaction between a=3FTF|1|C|A|1519 B=3FTF|1|D|G|1516
  6 Basepair  1519 1516 AG tHS 
No need to probe because of interaction between a=3FTF|1|C|C|1520 B=3FTF|1|D|G|1515
  7 Basepair  1520 1515 CG cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1515 - C1520 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1516 - A1519 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1517 - A1518 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1518 - G1517 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1519 - G1516 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1520 - G1515 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_06136.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.5549
   -9.5549
   -9.5549
   -9.8466
   -9.8466
  -12.7859

Timestamp 18-Jul-2025 22:46:40
pMakeSCFGModels: Making JAR3D model for motif group IL_06300.1, number 28 of 411
pMakeNodes starting loop:     a=4WF9|1|X|U|889 B=4WF9|1|X|A|978
  2 Basepair   889  978 UA cWW 
No need to probe because of interaction between a=4WF9|1|X|G|890 B=4WF9|1|X|A|977
  3 Basepair   890  977 GA cSW 
pMakeNodes probe for inserts:  a=4WF9|1|X|A|891 B=4WF9|1|X|U|976
    Insertion on left  4WF9|1|X|A|891
    Insertion on left  4WF9|1|X|U|892
    Insertion on right 4WF9|1|X|U|976
pMakeNodesProbeForInsertions:  a 4WF9|1|X|G|893 interacts with 4WF9|1|X|U|975
pMakeNodesProbeForInsertions:  B 4WF9|1|X|U|975 interacts with 4WF9|1|X|G|893
pMakeNodesProbeForInsertions:  B 4WF9|1|X|U|975 interacts with 4WF9|1|X|G|893
pMakeNodes probed for insert:  a=4WF9|1|X|G|893 B=4WF9|1|X|U|975
  4 Basepair   893  975 GU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|A|891
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|U|892
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WF9|1|X|U|976
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U889 - A978 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAU'
           RightLetter: 'UA'
               Comment: ' // Basepair G890 - A977 cSW '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|A|891'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|U|892'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WF9|1|X|U|976'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G893 - U975 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_06300.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.5781

Timestamp 18-Jul-2025 22:46:40
pMakeSCFGModels: Making JAR3D model for motif group IL_06549.2, number 29 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|G|907 B=8P9A|1|AR|C|923
  2 Basepair   907  923 GC cWW 
No need to probe because of interaction between a=8P9A|1|AR|G|909 B=8P9A|1|AR|U|919
  3 Basepair   909  919 GU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  2
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G907 - C923 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G909 - U919 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 3
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  2
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_06549.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1034
   -6.1034
   -6.5216
   -6.0151
   -6.5216
   -7.3144

Timestamp 18-Jul-2025 22:46:40
pMakeSCFGModels: Making JAR3D model for motif group IL_06691.1, number 30 of 411
pMakeNodes starting loop:     a=5J7L|1|AA|G|1144 B=5J7L|1|AA|C|1128
pMakeNodes making a cluster near strand break a=5J7L|1|AA|G|1144 B=5J7L|1|AA|C|1128
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 8 to 10
aa is 5 bb is 8
  2 Cluster   5J7L|1|AA|G|1144:5J7L|1|AA|U|1148 5J7L|1|AA|U|1125:5J7L|1|AA|C|1128
    LR Inter  5J7L|1|AA|A|1145 5J7L|1|AA|U|1125 tWH 
    LR Inter  5J7L|1|AA|U|1148 5J7L|1|AA|U|1125 cWW 
    LR Inter  5J7L|1|AA|A|1145 5J7L|1|AA|G|1127 cWW 
    LR Inter  5J7L|1|AA|G|1144 5J7L|1|AA|C|1128 cWW 
    LR Inter  5J7L|1|AA|C|1147 5J7L|1|AA|C|1128 cWS 
    LL Inter  5J7L|1|AA|G|1144 5J7L|1|AA|A|1146 tSW 
    LL Inter  5J7L|1|AA|A|1145 5J7L|1|AA|C|1147 cSH 
    LL Inter  5J7L|1|AA|A|1145 5J7L|1|AA|U|1148 tSW 
pMakeNodesCluster a=6 B=7 at the end
pMakeNodesCluster a=6 B=7 at the end
No need to probe because of interaction between a=5J7L|1|AA|C|1149 B=5J7L|1|AA|G|1124
  3 Basepair  1149 1124 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  8  9 10
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 0 0 0 0 1 1 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: [8 9 10]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAACU'
           RightLetter: 'UGC'
               Comment: ' // Cluster node 5J7L|1|AA|G|1144:5J7L|1|AA|U|1148 and 5J7L|1|AA|U|1125:5J7L|1|AA|C|1128'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 3.5625e-05
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1149 - G1124 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  8  9 10
pMakeMotifModelFromSSF:   3   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pConservedInteractionList: did not find a substitution probability matrix for cSH  between 7 and 8
pConservedInteractionList: did not find a substitution probability matrix for cSH  between 7 and 8
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_06691.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.0830
   -6.0145

Timestamp 18-Jul-2025 22:46:42
pMakeSCFGModels: Making JAR3D model for motif group IL_07039.3, number 31 of 411
pMakeNodes starting loop:     a=4V9F|1|0|U|2615 B=4V9F|1|0|G|2543
  2 Basepair  2615 2543 UG cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|G|2616 B=4V9F|1|0|C|2542
    Insertion on left  4V9F|1|0|G|2616
pMakeNodesProbeForInsertions:  a 4V9F|1|0|G|2617 interacts with 4V9F|1|0|C|2542
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|2542 interacts with 4V9F|1|0|G|2617
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|2542 interacts with 4V9F|1|0|G|2617
pMakeNodes probed for insert:  a=4V9F|1|0|G|2617 B=4V9F|1|0|C|2542
  3 Basepair  2617 2542 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|G|2543
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UG'
           RightLetter: 'G'
               Comment: ' // Basepair U2615 - G2543 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|G|2543'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2617 - C2542 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_07039.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.1610
   -3.1610
   -3.1610
   -3.1610
   -3.1610
   -3.1610
   -5.6571
   -5.1463
   -5.1463
   -3.1610
   -3.4097
   -3.6917
   -3.6917
   -3.6917
   -3.6917
   -3.6917

Timestamp 18-Jul-2025 22:46:42
pMakeSCFGModels: Making JAR3D model for motif group IL_07171.1, number 32 of 411
pMakeNodes starting loop:     a=4V9F|1|0|A|2746 B=4V9F|1|0|U|2733
  2 Basepair  2746 2733 AU cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|C|2747 B=4V9F|1|0|U|2732
    Insertion on left  4V9F|1|0|C|2747
    Insertion on left  4V9F|1|0|G|2748
pMakeNodesProbeForInsertions:  a 4V9F|1|0|G|2750 interacts with 4V9F|1|0|U|2732
pMakeNodesProbeForInsertions:  B 4V9F|1|0|U|2732 interacts with 4V9F|1|0|G|2750
pMakeNodesProbeForInsertions:  B 4V9F|1|0|U|2732 interacts with 4V9F|1|0|G|2750
pMakeNodes probed for insert:  a=4V9F|1|0|G|2750 B=4V9F|1|0|U|2732
  3 Basepair  2750 2732 GU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|U|2733
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|2746
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'ACG'
           RightLetter: 'U'
               Comment: ' // Basepair A2746 - U2733 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|U|2733'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|A|2746'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G2750 - U2732 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_07171.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.8363

Timestamp 18-Jul-2025 22:46:43
pMakeSCFGModels: Making JAR3D model for motif group IL_07173.1, number 33 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|A|1355 B=8CRE|1|CM|U|1338
  2 Basepair  1355 1338 AU cWW 
pMakeNodes probe for inserts:  a=8CRE|1|CM|A|1357 B=8CRE|1|CM|C|1337
    Insertion on left  8CRE|1|CM|A|1357
    Insertion on left  8CRE|1|CM|G|1358
    Insertion on left  8CRE|1|CM|U|1359
    Insertion on right 8CRE|1|CM|C|1337
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|C|1360 interacts with 8CRE|1|CM|G|1336
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|1336 interacts with 8CRE|1|CM|C|1360
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|1336 interacts with 8CRE|1|CM|C|1360
pMakeNodes probed for insert:  a=8CRE|1|CM|C|1360 B=8CRE|1|CM|G|1336
  3 Basepair  1360 1336 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|C|1337
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|U|1338
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|A|1355
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|CM|G|1358
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAGU'
           RightLetter: 'CU'
               Comment: ' // Basepair A1355 - U1338 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|C|1337'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|U|1338'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|A|1355'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|CM|G|1358'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1360 - G1336 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_07173.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.2247

Timestamp 18-Jul-2025 22:46:43
pMakeSCFGModels: Making JAR3D model for motif group IL_07469.2, number 34 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|U|2909 B=8P9A|1|AR|A|2892
  2 Basepair  2909 2892 UA cWW 
No need to probe because of interaction between a=8P9A|1|AR|A|2910 B=8P9A|1|AR|U|2891
pMakeNodes making a cluster near strand break a=8P9A|1|AR|A|2910 B=8P9A|1|AR|U|2891
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 6 and then 7 to 9
aa is 6 bb is 7
  3 Cluster   8P9A|1|AR|A|2910:8P9A|1|AR|G|2914 8P9A|1|AR|C|2889:8P9A|1|AR|U|2891
    LR Inter  8P9A|1|AR|A|2911 8P9A|1|AR|C|2889 bif 
    LR Inter  8P9A|1|AR|G|2914 8P9A|1|AR|C|2889 cWW 
    LR Inter  8P9A|1|AR|C|2913 8P9A|1|AR|A|2890 cWW 
    LR Inter  8P9A|1|AR|A|2910 8P9A|1|AR|U|2891 tSH 
    LR Inter  8P9A|1|AR|G|2912 8P9A|1|AR|U|2891 cWW 
    LL Inter  8P9A|1|AR|A|2911 8P9A|1|AR|G|2914 cSH 
pMakeNodesCluster a=7 B=6 at the end
pMakeNodesCluster a=7 B=6 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6 Right  7  8  9
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U2909 - A2892 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5 6]
            RightIndex: [7 8 9]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAGCG'
           RightLetter: 'CAU'
               Comment: ' // Cluster node 8P9A|1|AR|A|2910:8P9A|1|AR|G|2914 and 8P9A|1|AR|C|2889:8P9A|1|AR|U|2891'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0121

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6 Right  7  8  9
pMakeMotifModelFromSSF:   4   Initial Left  7 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_07469.2 allow insertions from initial node 4?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_07469.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.5301
   -3.5301
  -10.4540

Timestamp 18-Jul-2025 22:46:43
pMakeSCFGModels: Making JAR3D model for motif group IL_07785.1, number 35 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|U|429 B=8P9A|1|AR|A|630
  2 Basepair   429  630 UA cWW 
No need to probe because of interaction between a=8P9A|1|AR|U|430 B=8P9A|1|AR|U|629
  3 Basepair   430  629 UU cWW 
No need to probe because of interaction between a=8P9A|1|AR|U|431 B=8P9A|1|AR|A|628
  4 Basepair   431  628 UA cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U429 - A630 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U430 - U629 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U431 - A628 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_07785.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.4427
   -5.3565
   -5.4284
   -5.9003
   -7.1708
   -5.2110
   -6.7155
   -7.3713
   -5.9003
   -6.7155
   -5.9003
   -5.9003
   -5.4284
   -5.1354
   -8.1034
   -7.2734
  -10.5553
   -8.2579
   -8.2579
   -7.4967
   -7.2721
   -7.8310
   -7.1237
   -7.4967
   -8.2579
   -8.2579
   -7.9066
   -8.8344
   -7.6663
   -7.1794
   -7.6154
   -7.6154
   -9.4422

Timestamp 18-Jul-2025 22:46:44
pMakeSCFGModels: Making JAR3D model for motif group IL_08770.1, number 36 of 411
pMakeNodes starting loop:     a=2ET8|1|A|G|15 B=2ET8|1|B|C|31
  2 Basepair    15   31 GC cWW 
pMakeNodes probe for inserts:  a=2ET8|1|A|A|17 B=2ET8|1|B|A|30
    Insertion on left  2ET8|1|A|A|17
    Insertion on right 2ET8|1|B|A|30
pMakeNodesProbeForInsertions:  a 2ET8|1|A|G|18 interacts with 2ET8|1|B|C|29
pMakeNodesProbeForInsertions:  B 2ET8|1|B|C|29 interacts with 2ET8|1|A|G|18
pMakeNodesProbeForInsertions:  B 2ET8|1|B|C|29 interacts with 2ET8|1|A|G|18
pMakeNodes probed for insert:  a=2ET8|1|A|G|18 B=2ET8|1|B|C|29
  3 Basepair    18   29 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2ET8|1|A|A|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 2ET8|1|B|C|29
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'AC'
               Comment: ' // Basepair G15 - C31 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2ET8|1|A|A|16'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 2ET8|1|B|C|29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G18 - C29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_08770.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3207
   -6.3207
   -8.3477
   -6.0197
   -6.4540

Timestamp 18-Jul-2025 22:46:44
pMakeSCFGModels: Making JAR3D model for motif group IL_09044.1, number 37 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|U|1540 B=9DFE|1|1A|G|1529
  2 Basepair  1540 1529 UG cWW 
No need to probe because of interaction between a=9DFE|1|1A|G|1541 B=9DFE|1|1A|A|1528|||A
  3 Basepair  1541 1528A GA tSH 
No need to probe because of interaction between a=9DFE|1|1A|A|1542 B=9DFE|1|1A|A|1528
  4 Basepair  1542 1528 AA tHH 
pMakeNodes probe for inserts:  a=9DFE|1|1A|A|1544 B=9DFE|1|1A|G|1527
    Insertion on left  9DFE|1|1A|A|1544
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|A|1545 interacts with 9DFE|1|1A|G|1527
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|G|1527 interacts with 9DFE|1|1A|A|1545
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|G|1527 interacts with 9DFE|1|1A|A|1545
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=9DFE|1|1A|A|1545 B=9DFE|1|1A|G|1527
  5 Basepair  1545 1527 AG tHS 
No need to probe because of interaction between a=9DFE|1|1A|C|1546 B=9DFE|1|1A|G|1526
  6 Basepair  1546 1526 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|A|1528|||A
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U1540 - G1529 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1541 - A1528A tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'A'
               Comment: ' // Basepair A1542 - A1528 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|A|1528|||A'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1545 - G1527 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1546 - G1526 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_09044.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4802

Timestamp 18-Jul-2025 22:46:45
pMakeSCFGModels: Making JAR3D model for motif group IL_09129.2, number 38 of 411
pMakeNodes starting loop:     a=4LFB|1|A|U|1247 B=4LFB|1|A|G|1290
  2 Basepair  1247 1290 UG cWW 
No need to probe because of interaction between a=4LFB|1|A|A|1248 B=4LFB|1|A|A|1289
  3 Basepair  1248 1289 AA tWH 
No need to probe because of interaction between a=4LFB|1|A|C|1249 B=4LFB|1|A|A|1288
  4 Basepair  1249 1288 CA tWH 
pMakeNodes probe for inserts:  a=4LFB|1|A|A|1250 B=4LFB|1|A|A|1287
    Insertion on left  4LFB|1|A|A|1250
    Insertion on left  4LFB|1|A|A|1251
    Insertion on right 4LFB|1|A|A|1287
    Insertion on right 4LFB|1|A|A|1286
pMakeNodesProbeForInsertions:  a 4LFB|1|A|A|1252 interacts with 4LFB|1|A|A|1285
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|1285 interacts with 4LFB|1|A|A|1252
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|1285 interacts with 4LFB|1|A|A|1252
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4LFB|1|A|A|1252 B=4LFB|1|A|A|1285
  5 Basepair  1252 1285 AA tWW 
No need to probe because of interaction between a=4LFB|1|A|G|1253 B=4LFB|1|A|C|1284
  6 Basepair  1253 1284 GC cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|1250
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|1251
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|A|1287
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|A|1286
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U1247 - G1290 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A1248 - A1289 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAA'
           RightLetter: 'AAA'
               Comment: ' // Basepair C1249 - A1288 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|1250'
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|1251'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|A|1287'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|A|1286'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A1252 - A1285 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1253 - C1284 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  15   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a hairpin at node 15

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_09129.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8645
   -7.8645

Timestamp 18-Jul-2025 22:46:45
pMakeSCFGModels: Making JAR3D model for motif group IL_09570.1, number 39 of 411
pMakeNodes starting loop:     a=1YLS|1|B|G|207 B=1YLS|1|A|C|105
  2 Basepair   207  105 GC cWW 
pMakeNodes probe for inserts:  a=1YLS|1|B|G|208 B=1YLS|1|A|G|104
    Insertion on left  1YLS|1|B|G|208
    Insertion on left  1YLS|1|B|CSL|209
    Insertion on left  1YLS|1|B|C|210
    Insertion on left  1YLS|1|B|G|211
    Insertion on left  1YLS|1|B|U|212
    Insertion on left  1YLS|1|B|G|213
    Insertion on right 1YLS|1|A|G|104
    Insertion on right 1YLS|1|A|A|103
pMakeNodesProbeForInsertions:  a 1YLS|1|B|C|214 interacts with 1YLS|1|A|G|102
pMakeNodesProbeForInsertions:  B 1YLS|1|A|G|102 interacts with 1YLS|1|B|C|214
pMakeNodesProbeForInsertions:  B 1YLS|1|A|G|102 interacts with 1YLS|1|B|C|214
pMakeNodes probed for insert:  a=1YLS|1|B|C|214 B=1YLS|1|A|G|102
  3 Basepair   214  102 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   4   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1YLS|1|A|A|103
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1YLS|1|A|G|104
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1YLS|1|A|C|105
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1YLS|1|B|G|207
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1YLS|1|B|G|208
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1YLS|1|B|CSL|209
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1YLS|1|B|G|213
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1YLS|1|B|U|212
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGCCGUG'
           RightLetter: 'AGC'
               Comment: ' // Basepair G207 - C105 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1YLS|1|A|A|103'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1YLS|1|A|G|104'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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                  lpar: []
                  rpar: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1YLS|1|A|C|105'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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                  lpar: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
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                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1YLS|1|B|G|207'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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                  lpar: []
                  rpar: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                IBases: []
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                  lpar: []
                  rpar: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1YLS|1|B|G|208'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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                  lpar: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1YLS|1|B|CSL|209'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1YLS|1|B|G|213'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1YLS|1|B|U|212'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C214 - G102 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 22
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 11
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  17     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  18   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  19  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  20   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Found a hairpin at node 20

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_09570.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.7071

Timestamp 18-Jul-2025 22:46:46
pMakeSCFGModels: Making JAR3D model for motif group IL_09705.15, number 40 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|2350 B=5J7L|1|DA|G|2367
  2 Basepair  2350 2367 CG cWW 
No need to probe because of interaction between a=5J7L|1|DA|G|2351 B=5J7L|1|DA|A|2366
  3 Basepair  2351 2366 GA tSH 
No need to probe because of interaction between a=5J7L|1|DA|A|2352 B=5J7L|1|DA|G|2365
  4 Basepair  2352 2365 AG tHS 
No need to probe because of interaction between a=5J7L|1|DA|G|2353 B=5J7L|1|DA|C|2364
  5 Basepair  2353 2364 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2350 - G2367 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G2351 - A2366 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A2352 - G2365 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2353 - C2364 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_09705.15_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.0731
   -5.0731
   -5.0731
   -5.0731
   -6.0199
   -5.5725
   -6.6050
   -6.0199
   -6.4249
   -6.6050
   -5.0731
   -5.0731
   -5.7155
   -5.0731
   -7.3648
   -6.0199
   -5.6582
   -5.7155
   -6.2727
   -5.5354
   -6.2871
   -6.2727
   -5.5354
   -6.1487
   -6.7597
   -6.1487
   -6.3616
  -10.6227
  -10.6227
   -5.0731
   -7.7032
   -5.5152
   -5.5152
   -5.0731

Timestamp 18-Jul-2025 22:46:47
pMakeSCFGModels: Making JAR3D model for motif group IL_09908.1, number 41 of 411
pMakeNodes starting loop:     a=1U6B|1|C|C|197 B=1U6B|1|B|G|184
  2 Basepair   197  184 CG cWW 
pMakeNodes probe for inserts:  a=1U6B|1|C|A|198 B=1U6B|1|B|A|183
    Insertion on left  1U6B|1|C|A|198
    Insertion on left  1U6B|1|C|C|199
    Insertion on left  1U6B|1|C|A|200
pMakeNodesProbeForInsertions:  a 1U6B|1|C|A|201 interacts with 1U6B|1|B|A|183
pMakeNodesProbeForInsertions:  B 1U6B|1|B|A|183 interacts with 1U6B|1|C|A|201
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 1U6B|1|B|A|183 interacts with 1U6B|1|C|A|201
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=1U6B|1|C|A|201 B=1U6B|1|B|A|183
  3 Basepair   201  183 AA tHH 
No need to probe because of interaction between a=1U6B|1|C|A|202 B=1U6B|1|B|G|182
  4 Basepair   202  182 AG tHS 
No need to probe because of interaction between a=1U6B|1|C|C|203 B=1U6B|1|B|G|181
  5 Basepair   203  181 CG cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U6B|1|B|G|182
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U6B|1|B|A|183
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U6B|1|B|G|184
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CACA'
           RightLetter: 'G'
               Comment: ' // Basepair C197 - G184 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U6B|1|B|G|182'
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U6B|1|B|A|183'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U6B|1|B|G|184'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A201 - A183 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A202 - G182 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C203 - G181 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  12   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_09908.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0125

Timestamp 18-Jul-2025 22:46:47
pMakeSCFGModels: Making JAR3D model for motif group IL_09990.4, number 42 of 411
pMakeNodes starting loop:     a=4V9F|1|0|G|1475 B=4V9F|1|0|C|1467
  2 Basepair  1475 1467 GC cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|1476 B=4V9F|1|0|C|1466
    Insertion on left  4V9F|1|0|A|1476
pMakeNodesProbeForInsertions:  a 4V9F|1|0|C|1477 interacts with 4V9F|1|0|C|1466
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|1466 interacts with 4V9F|1|0|C|1477
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|1466 interacts with 4V9F|1|0|C|1477
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4V9F|1|0|C|1477 B=4V9F|1|0|C|1466
  3 Basepair  1477 1466 CC bif 
No need to probe because of interaction between a=4V9F|1|0|U|1478 B=4V9F|1|0|A|1465
  4 Basepair  1478 1465 UA cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|C|1466
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'C'
               Comment: ' // Basepair G1475 - C1467 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|C|1466'
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C1477 - C1466 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1478 - A1465 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_09990.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.4480
   -6.2988

Timestamp 18-Jul-2025 22:46:47
pMakeSCFGModels: Making JAR3D model for motif group IL_10167.6, number 43 of 411
pMakeNodes starting loop:     a=3R1C|1|Q|C|5 B=3R1C|1|R|G|4
  2 Basepair     5    4 CG cWW 
No need to probe because of interaction between a=3R1C|1|Q|G|6 B=3R1C|1|R|G|3
  3 Basepair     6    3 GG cHW 
No need to probe because of interaction between a=3R1C|1|Q|G|7 B=3R1C|1|R|C|2
  4 Basepair     7    2 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C5 - G4 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G6 - G3 cHW '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G7 - C2 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 1 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 2 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 3 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 4 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 5 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 6 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 7 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 8 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 9 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 11 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 13 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 14 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 15 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 16 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 17 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 18 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 19 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 20 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 21 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 22 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 24 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 26 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 29 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 32 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 34 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 35 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 37 of 51, pair 2,5 for nucleotide 2 (A) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 38 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 39 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 40 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 41 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 42 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 43 of 51, pair 2,5 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 49 of 51, pair 2,5 for nucleotide 2 (A) making self BPh with edge 1
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_10167.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.9779
   -2.9779
   -2.9779
   -2.9779
   -3.9194
   -2.9779
   -2.9779
   -2.9779
   -3.8959
   -2.9779
   -2.9779
   -3.6220
   -3.9194
   -2.9779
   -2.9779
   -2.9779
   -2.9779
   -2.9779
   -2.9779
   -3.9194
   -6.0066
   -3.9194
   -5.4804
   -3.2336
   -3.6220
   -5.4804
   -3.6220
   -6.2393
   -2.9779
   -6.2393
   -3.6220
   -2.9779
   -3.6220
   -3.2336
   -6.0066
   -2.9779
   -6.7064
   -3.7148
   -5.5654
   -5.5654
   -3.7148
   -3.4592
   -3.7148
   -7.0382
   -5.4804
   -5.4804
  -13.7095
   -7.4735
  -11.8490
   -5.4804
   -7.3590

Timestamp 18-Jul-2025 22:46:48
pMakeSCFGModels: Making JAR3D model for motif group IL_10389.1, number 44 of 411
pMakeNodes starting loop:     a=4R4V|1|A|G|749 B=4R4V|1|A|C|726
  2 Basepair   749  726 GC cWW 
pMakeNodes probe for inserts:  a=4R4V|1|A|C|750 B=4R4V|1|A|A|725
    Insertion on left  4R4V|1|A|C|750
    Insertion on left  4R4V|1|A|A|751
pMakeNodesProbeForInsertions:  a 4R4V|1|A|G|752 interacts with 4R4V|1|A|A|725
pMakeNodesProbeForInsertions:  B 4R4V|1|A|A|725 interacts with 4R4V|1|A|G|752
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4R4V|1|A|A|725 interacts with 4R4V|1|A|G|752
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4R4V|1|A|G|752 B=4R4V|1|A|A|725
  3 Basepair   752  725 GA cWW 
No need to probe because of interaction between a=4R4V|1|A|C|753 B=4R4V|1|A|G|724
  4 Basepair   753  724 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4R4V|1|A|A|725
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4R4V|1|A|C|726
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GCA'
           RightLetter: 'C'
               Comment: ' // Basepair G749 - C726 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4R4V|1|A|A|725'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4R4V|1|A|C|726'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G752 - A725 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C753 - G724 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_10389.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.9051
   -8.0816

Timestamp 18-Jul-2025 22:46:49
pMakeSCFGModels: Making JAR3D model for motif group IL_10484.1, number 45 of 411
pMakeNodes starting loop:     a=6E7L|1|A|U|10 B=6E7L|1|A|G|13||||7_375
  2 Basepair    10   13 UG cWW 
No need to probe because of interaction between a=6E7L|1|A|U|11 B=6E7L|1|A|C|12||||7_375
  3 Basepair    11   12 UC tSH 
No need to probe because of interaction between a=6E7L|1|A|C|12 B=6E7L|1|A|U|11||||7_375
  4 Basepair    12   11 CU tHS 
No need to probe because of interaction between a=6E7L|1|A|G|13 B=6E7L|1|A|U|10||||7_375
  5 Basepair    13   10 GU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U10 - G13 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'C'
               Comment: ' // Basepair U11 - C12 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'U'
               Comment: ' // Basepair C12 - U11 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G13 - U10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_10484.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.9368
   -6.4236

Timestamp 18-Jul-2025 22:46:49
pMakeSCFGModels: Making JAR3D model for motif group IL_10569.1, number 46 of 411
pMakeNodes starting loop:     a=1HYS|1|E|A|867 B=1HYS|1|F|DT|887
  2 Basepair   867  887 AU cWW 
No need to probe because of interaction between a=1HYS|1|E|A|868 B=1HYS|1|F|DT|886
pMakeNodes making a cluster near strand break a=1HYS|1|E|A|868 B=1HYS|1|F|DT|886
pMakeNodesCluster: amax is 3 bmin is 4, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 3 and then 4 to 4
aa is 3 bb is 4
  3 Cluster   1HYS|1|E|A|868:1HYS|1|E|A|869 1HYS|1|F|DT|886:1HYS|1|F|DT|886
    LR Inter  1HYS|1|E|A|868 1HYS|1|F|DT|886 cWW 
    LR Inter  1HYS|1|E|A|869 1HYS|1|F|DT|886 cWW 
pMakeNodesCluster a=4 B=3 at the end
pMakeNodesCluster a=4 B=3 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A867 - U887 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3]
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AA'
           RightLetter: 'U'
               Comment: ' // Cluster node 1HYS|1|E|A|868:1HYS|1|E|A|869 and 1HYS|1|F|DT|886:1HYS|1|F|DT|886'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2517

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  3
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_10569.1 allow insertions from initial node 4?
ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_10569.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.8359
   -3.5532

Timestamp 18-Jul-2025 22:46:49
pMakeSCFGModels: Making JAR3D model for motif group IL_10796.1, number 47 of 411
pMakeNodes starting loop:     a=4O41|1|C|URU|306 B=4O41|1|D|G|409
  2 Basepair   306  409 UG cWW 
pMakeNodes probe for inserts:  a=4O41|1|C|C|308 B=4O41|1|D|C|408
    Insertion on left  4O41|1|C|C|308
    Insertion on right 4O41|1|D|C|408
pMakeNodesProbeForInsertions:  a 4O41|1|C|G|309 interacts with 4O41|1|D|URU|406
pMakeNodesProbeForInsertions:  B 4O41|1|D|URU|406 interacts with 4O41|1|C|G|309
pMakeNodesProbeForInsertions:  B 4O41|1|D|URU|406 interacts with 4O41|1|C|G|309
pMakeNodes probed for insert:  a=4O41|1|C|G|309 B=4O41|1|D|URU|406
  3 Basepair   309  406 GU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4O41|1|C|C|308
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4O41|1|D|C|408
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UC'
           RightLetter: 'CG'
               Comment: ' // Basepair U306 - G409 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4O41|1|C|C|308'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4O41|1|D|C|408'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G309 - U406 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_10796.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.5911

Timestamp 18-Jul-2025 22:46:50
pMakeSCFGModels: Making JAR3D model for motif group IL_11344.2, number 48 of 411
pMakeNodes starting loop:     a=4LFB|1|A|C|1277 B=4LFB|1|A|G|1258
  2 Basepair  1277 1258 CG cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|A|1279 B=4LFB|1|A|G|1255
    Insertion on left  4LFB|1|A|A|1279
pMakeNodesProbeForInsertions:  a 4LFB|1|A|C|1282 interacts with 4LFB|1|A|G|1255
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|1255 interacts with 4LFB|1|A|C|1282
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|1255 interacts with 4LFB|1|A|C|1282
pMakeNodes probed for insert:  a=4LFB|1|A|C|1282 B=4LFB|1|A|G|1255
  3 Basepair  1282 1255 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|1256
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: 'G'
               Comment: ' // Basepair C1277 - G1258 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|1256'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1282 - G1255 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_11344.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.2558
   -8.4085

Timestamp 18-Jul-2025 22:46:50
pMakeSCFGModels: Making JAR3D model for motif group IL_11399.2, number 49 of 411
pMakeNodes starting loop:     a=9J6P|1|B|A|16 B=9J6P|1|A|U|9
  2 Basepair    16    9 AU cWW 
No need to probe because of interaction between a=9J6P|1|B|G|17 B=9J6P|1|A|G|8
  3 Basepair    17    8 GG cHW 
pMakeNodes probe for inserts:  a=9J6P|1|B|G|18 B=9J6P|1|A|G|7
    Insertion on left  9J6P|1|B|G|18
    Insertion on left  9J6P|1|B|A|19
    Insertion on right 9J6P|1|A|G|7
pMakeNodesProbeForInsertions:  a 9J6P|1|B|C|20 interacts with 9J6P|1|A|G|6
pMakeNodesProbeForInsertions:  B 9J6P|1|A|G|6 interacts with 9J6P|1|B|C|20
pMakeNodesProbeForInsertions:  B 9J6P|1|A|G|6 interacts with 9J6P|1|B|C|20
pMakeNodes probed for insert:  a=9J6P|1|B|C|20 B=9J6P|1|A|G|6
  4 Basepair    20    6 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9J6P|1|A|G|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9J6P|1|A|U|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 9J6P|1|B|G|18
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A16 - U9 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGA'
           RightLetter: 'GG'
               Comment: ' // Basepair G17 - G8 cHW '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9J6P|1|A|G|8'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9J6P|1|A|U|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 9J6P|1|B|G|18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C20 - G6 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 11
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 1 of 3, pair 2,8 for nucleotide 2 (G) making self BPh with edge 1
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 2 of 3, pair 2,8 for nucleotide 2 (G) making self BPh with edge 1
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_11399.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.7105
   -4.7105
   -7.8520

Timestamp 18-Jul-2025 22:46:50
pMakeSCFGModels: Making JAR3D model for motif group IL_11415.1, number 50 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|U|1014 B=8P9A|1|AR|A|1036
  2 Basepair  1014 1036 UA cWW 
No need to probe because of interaction between a=8P9A|1|AR|U|1015 B=8P9A|1|AR|G|1035
  3 Basepair  1015 1035 UG bif 
pMakeNodes probe for inserts:  a=8P9A|1|AR|C|1016 B=8P9A|1|AR|U|1034
    Insertion on left  8P9A|1|AR|C|1016
    Insertion on left  8P9A|1|AR|C|1017
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|G|1018 interacts with 8P9A|1|AR|U|1034
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|U|1034 interacts with 8P9A|1|AR|G|1018
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|U|1034 interacts with 8P9A|1|AR|G|1018
pMakeNodes probed for insert:  a=8P9A|1|AR|G|1018 B=8P9A|1|AR|U|1034
  4 Basepair  1018 1034 GU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|C|1016
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|C|1017
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1014 - A1036 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UCC'
           RightLetter: 'G'
               Comment: ' // Basepair U1015 - G1035 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|C|1016'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|C|1017'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1018 - U1034 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_11415.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.5092

Timestamp 18-Jul-2025 22:46:51
pMakeSCFGModels: Making JAR3D model for motif group IL_12566.4, number 51 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|G|1651 B=5J7L|1|DA|C|2006
  2 Basepair  1651 2006 GC cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|1652 B=5J7L|1|DA|A|2005
    Insertion on left  5J7L|1|DA|A|1652
    Insertion on left  5J7L|1|DA|G|1653
    Insertion on left  5J7L|1|DA|A|1654
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|A|1655 interacts with 5J7L|1|DA|A|2005
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|2005 interacts with 5J7L|1|DA|A|1655
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|2005 interacts with 5J7L|1|DA|A|1655
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5J7L|1|DA|A|1655 B=5J7L|1|DA|A|2005
  3 Basepair  1655 2005 AA tHS 
No need to probe because of interaction between a=5J7L|1|DA|C|1656 B=5J7L|1|DA|G|2004
  4 Basepair  1656 2004 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|1652
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|1653
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|1654
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAGA'
           RightLetter: 'C'
               Comment: ' // Basepair G1651 - C2006 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|1652'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|1653'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|1654'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A1655 - A2005 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1656 - G2004 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_12566.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.8264
   -3.8264
   -3.8264
   -4.9250
   -7.2405

Timestamp 18-Jul-2025 22:46:51
pMakeSCFGModels: Making JAR3D model for motif group IL_12697.1, number 52 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|U|37 B=8CRE|1|CM|A|469
  2 Basepair    37  469 UA cWW 
No need to probe because of interaction between a=8CRE|1|CM|C|38 B=8CRE|1|CM|A|468
  3 Basepair    38  468 CA cWW 
No need to probe because of interaction between a=8CRE|1|CM|A|39 B=8CRE|1|CM|C|467
  4 Basepair    39  467 AC tSH 
No need to probe because of interaction between a=8CRE|1|CM|A|40 B=8CRE|1|CM|G|465
  5 Basepair    40  465 AG tHS 
No need to probe because of interaction between a=8CRE|1|CM|A|41 B=8CRE|1|CM|U|464
  6 Basepair    41  464 AU cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U37 - A469 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C38 - A468 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A39 - C467 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A40 - G465 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A41 - U464 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_12697.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.9241
   -7.9241

Timestamp 18-Jul-2025 22:46:51
pMakeSCFGModels: Making JAR3D model for motif group IL_12745.1, number 53 of 411
pMakeNodes starting loop:     a=4LFB|1|A|G|148 B=4LFB|1|A|C|174
  2 Basepair   148  174 GC cWW 
No need to probe because of interaction between a=4LFB|1|A|A|149 B=4LFB|1|A|A|172
  3 Basepair   149  172 AA tWH 
No need to probe because of interaction between a=4LFB|1|A|C|150 B=4LFB|1|A|A|171
  4 Basepair   150  171 CA tWH 
No need to probe because of interaction between a=4LFB|1|A|A|151 B=4LFB|1|A|U|170
  5 Basepair   151  170 AU tHW 
No need to probe because of interaction between a=4LFB|1|A|A|152 B=4LFB|1|A|C|169
  6 Basepair   152  169 AC tHW 
No need to probe because of interaction between a=4LFB|1|A|C|153 B=4LFB|1|A|G|168
  7 Basepair   153  168 CG cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G148 - C174 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A149 - A172 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C150 - A171 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A151 - U170 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A152 - C169 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C153 - G168 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_12745.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7221

Timestamp 18-Jul-2025 22:46:52
pMakeSCFGModels: Making JAR3D model for motif group IL_13358.1, number 54 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|U|245 B=8P9A|1|AR|G|173
  2 Basepair   245  173 UG cWW 
No need to probe because of interaction between a=8P9A|1|AR|U|246 B=8P9A|1|AR|G|172
  3 Basepair   246  172 UG cWW 
pMakeNodes probe for inserts:  a=8P9A|1|AR|C|247 B=8P9A|1|AR|G|171
    Insertion on left  8P9A|1|AR|C|247
    Insertion on left  8P9A|1|AR|U|248
    Insertion on left  8P9A|1|AR|U|249
    Insertion on left  8P9A|1|AR|U|250
    Insertion on left  8P9A|1|AR|G|251
    Insertion on right 8P9A|1|AR|G|171
    Insertion on right 8P9A|1|AR|G|170
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|A|253 interacts with 8P9A|1|AR|U|169
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|U|169 interacts with 8P9A|1|AR|A|253
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|U|169 interacts with 8P9A|1|AR|A|253
pMakeNodes probed for insert:  a=8P9A|1|AR|A|253 B=8P9A|1|AR|U|169
  4 Basepair   253  169 AU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|G|171
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|G|172
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|G|173
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|U|245
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|U|246
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|U|250
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|U|249
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U245 - G173 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UCUUUG'
           RightLetter: 'GGG'
               Comment: ' // Basepair U246 - G172 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|G|171'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|G|172'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|G|173'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|U|245'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|U|246'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|U|250'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|U|249'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 19
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A253 - U169 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 21
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 11
pMakeMotifModelFromSSF:  15   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  16     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  17   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  18  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  19   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Found a hairpin at node 19

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_13358.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.9956

Timestamp 18-Jul-2025 22:46:52
pMakeSCFGModels: Making JAR3D model for motif group IL_13394.1, number 55 of 411
pMakeNodes starting loop:     a=5J7L|1|AA|A|1021 B=5J7L|1|AA|U|1008
  2 Basepair  1021 1008 AU cWW 
pMakeNodes probe for inserts:  a=5J7L|1|AA|A|1022 B=5J7L|1|AA|U|1007
    Insertion on left  5J7L|1|AA|A|1022
    Insertion on left  5J7L|1|AA|U|1023
    Insertion on left  5J7L|1|AA|G|1024
    Insertion on left  5J7L|1|AA|U|1025
    Insertion on left  5J7L|1|AA|G|1026
    Insertion on left  5J7L|1|AA|C|1027
    Insertion on left  5J7L|1|AA|C|1028
    Insertion on right 5J7L|1|AA|U|1007
    Insertion on right 5J7L|1|AA|G|1006
    Insertion on right 5J7L|1|AA|A|1005
    Insertion on right 5J7L|1|AA|A|1004
pMakeNodesProbeForInsertions:  a 5J7L|1|AA|U|1029 interacts with 5J7L|1|AA|G|1032
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|G|1003 interacts with 5J7L|1|AA|C|1037
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|G|1003 interacts with 5J7L|1|AA|C|1037
pMakeNodes probed for insert:  a=5J7L|1|AA|U|1029 B=5J7L|1|AA|G|1003
pMakeNodes making a cluster near strand break a=5J7L|1|AA|U|1029 B=5J7L|1|AA|G|1003
pMakeNodesCluster: amax is 15 bmin is 16, use_amax is 1
pMakeNodesCluster: Cluster goes from 9 to 15 and then 16 to 16
aa is 15 bb is 16
  3 Cluster   5J7L|1|AA|U|1029:5J7L|1|AA|C|1037 5J7L|1|AA|G|1003:5J7L|1|AA|G|1003
    LR Inter  5J7L|1|AA|C|1037 5J7L|1|AA|G|1003 cWW 
    LL Inter  5J7L|1|AA|U|1029 5J7L|1|AA|G|1032 tSS 
    Left  strand conserved insertion 5J7L|1|AA|G|1033 at position 3
    Left  strand conserved insertion 5J7L|1|AA|G|1034 at position 4
    Left  strand conserved insertion 5J7L|1|AA|A|1035 at position 5
    Left  strand conserved insertion 5J7L|1|AA|A|1036 at position 6
pMakeNodesCluster a=16 B=15 at the end
pMakeNodesCluster a=16 B=15 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 21
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 21
pMakeMotifModelFromSSF:   3   Cluster Left  9 10 11 12 13 14 15 Right 16
pMakeMotifModelFromSSF:   4   Hairpin Left 16 Right 15
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|A|1004
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|A|1005
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|G|1006
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|U|1007
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|U|1008
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|A|1021
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|A|1022
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|AA|G|1034
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|AA|G|1033
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|AA|G|1032
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|AA|C|1031
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 21
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [21×21 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAUGUGCC'
           RightLetter: 'AAGUU'
               Comment: ' // Basepair A1021 - U1008 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|A|1004'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [3 4 5 6]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|A|1005'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 16
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|G|1006'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|U|1007'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|U|1008'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                  rpar: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|A|1021'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                  rpar: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|A|1022'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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                  rpar: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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                  rpar: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|AA|G|1034'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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                  rpar: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                  rpar: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 9
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|AA|G|1033'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
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              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 9
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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                  rpar: []
          LeftNotInter: []
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Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             LeftIndex: 9
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|AA|G|1032'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 9
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             LeftIndex: 9
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|AA|C|1031'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 9
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 26
             LeftIndex: [9 10 11 12 13 14 15]
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGGGAAC'
           RightLetter: 'G'
               Comment: ' // Cluster node 5J7L|1|AA|U|1029:5J7L|1|AA|C|1037 and 5J7L|1|AA|G|1003:5J7L|1|AA|G|1003'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [3 4 5 6]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             LeftIndex: 16
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 29
             LeftIndex: 16
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 16
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 21
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 21
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 20
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 20
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 20
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 20
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 20
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 20
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 20
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 20
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 20
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 20
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 20
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 20
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 20
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 20
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 20
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 19
pMakeMotifModelFromSSF:  19     Fixed Left  9 Right 19
pMakeMotifModelFromSSF:  20   Initial Left  9 Right 18
pMakeMotifModelFromSSF:  21     Fixed Left  9 Right 18
pMakeMotifModelFromSSF:  22   Initial Left  9 Right 17
pMakeMotifModelFromSSF:  23     Fixed Left  9 Right 17
pMakeMotifModelFromSSF:  24   Initial Left  9 Right 16
pMakeMotifModelFromSSF:  25   Cluster Left  9 10 11 12 13 14 15 Right 16
pMakeMotifModelFromSSF:  26   Initial Left 16 Right 15
pMakeMotifModelFromSSF:  27   Hairpin Left 16 Right 15
pNextNodeJunction: Found a hairpin at node 27
pUpdateModelWithSSF: IL_13394.1 allow insertions from initial node 26?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 27

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_13394.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -16.4920

Timestamp 18-Jul-2025 22:46:53
pMakeSCFGModels: Making JAR3D model for motif group IL_13404.2, number 56 of 411
pMakeNodes starting loop:     a=422D|1|A|U|7 B=422D|1|B|G|22
  2 Basepair     7   22 UG cWW 
No need to probe because of interaction between a=422D|1|A|U|8 B=422D|1|B|C|21
  3 Basepair     8   21 UC cWW 
No need to probe because of interaction between a=422D|1|A|C|9 B=422D|1|B|U|20
  4 Basepair     9   20 CU cWW 
No need to probe because of interaction between a=422D|1|A|G|10 B=422D|1|B|U|19
  5 Basepair    10   19 GU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U7 - G22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'C'
               Comment: ' // Basepair U8 - C21 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'U'
               Comment: ' // Basepair C9 - U20 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G10 - U19 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_13404.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.2188
   -4.2188
   -4.2188
   -4.2188
   -4.2188
   -4.2188
   -4.2188
   -4.2188
  -13.8375
   -9.5677

Timestamp 18-Jul-2025 22:46:53
pMakeSCFGModels: Making JAR3D model for motif group IL_13874.1, number 57 of 411
pMakeNodes starting loop:     a=7OAX|1|A|U|8 B=7OAX|1|A|G|45
  2 Basepair     8   45 UG cWW 
pMakeNodes probe for inserts:  a=7OAX|1|A|G|9 B=7OAX|1|A|C|44
pMakeNodesProbeForInsertions:  a 7OAX|1|A|G|9 interacts with 7OAX|1|A|G|12
pMakeNodesProbeForInsertions:  B 7OAX|1|A|C|44 interacts with 7OAX|1|A|G|10
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 7OAX|1|A|C|44 interacts with 7OAX|1|A|A|11
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=7OAX|1|A|G|9 B=7OAX|1|A|C|44
pMakeNodes making a cluster near strand break a=7OAX|1|A|G|9 B=7OAX|1|A|C|44
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 5 and then 10 to 11
aa is 5 bb is 10
  3 Cluster   7OAX|1|A|G|9:7OAX|1|A|G|12 7OAX|1|A|G|42:7OAX|1|A|C|44
    LR Inter  7OAX|1|A|G|12 7OAX|1|A|G|42 cWH 
    LR Inter  7OAX|1|A|G|10 7OAX|1|A|C|44 cWW 
    LR Inter  7OAX|1|A|A|11 7OAX|1|A|C|44 tHS 
    LL Inter  7OAX|1|A|G|10 7OAX|1|A|A|11 cSH 
    LL Inter  7OAX|1|A|G|9 7OAX|1|A|G|12 cWH 
pMakeNodesCluster a=6 B=9 at the end
pMakeNodesCluster a=6 B=9 at the end
No need to probe because of interaction between a=7OAX|1|A|G|13 B=7OAX|1|A|G|41
  4 Basepair    13   41 GG cHW 
No need to probe because of interaction between a=7OAX|1|A|G|15 B=7OAX|1|A|C|40
  5 Basepair    15   40 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5 Right 10 11
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U8 - G45 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5]
            RightIndex: [10 11]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGAG'
           RightLetter: 'GC'
               Comment: ' // Cluster node 7OAX|1|A|G|9:7OAX|1|A|G|12 and 7OAX|1|A|G|42:7OAX|1|A|C|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: [1 2]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0054

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G13 - G41 cHW '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G15 - C40 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5 Right 10 11
pMakeMotifModelFromSSF:   4   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_13874.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.8499

Timestamp 18-Jul-2025 22:46:54
pMakeSCFGModels: Making JAR3D model for motif group IL_14177.2, number 58 of 411
pMakeNodes starting loop:     a=4LFB|1|A|C|47 B=4LFB|1|A|G|361
  2 Basepair    47  361 CG cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|U|49 B=4LFB|1|A|A|360
    Insertion on left  4LFB|1|A|U|49
    Insertion on left  4LFB|1|A|A|50
    Insertion on right 4LFB|1|A|A|360
pMakeNodesProbeForInsertions:  a 4LFB|1|A|G|52 interacts with 4LFB|1|A|U|359
pMakeNodesProbeForInsertions:  B 4LFB|1|A|U|359 interacts with 4LFB|1|A|G|52
pMakeNodesProbeForInsertions:  B 4LFB|1|A|U|359 interacts with 4LFB|1|A|G|52
pMakeNodes probed for insert:  a=4LFB|1|A|G|52 B=4LFB|1|A|U|359
  3 Basepair    52  359 GU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|C|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|U|49
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|G|52
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CUA'
           RightLetter: 'AG'
               Comment: ' // Basepair C47 - G361 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|C|48'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|U|49'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|G|52'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G52 - U359 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_14177.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.3143
   -5.6413

Timestamp 18-Jul-2025 22:46:54
pMakeSCFGModels: Making JAR3D model for motif group IL_14368.1, number 59 of 411
pMakeNodes starting loop:     a=5VCI|1|A|C|8 B=5VCI|1|B|G|5
  2 Basepair     8    5 CG cWW 
pMakeNodes probe for inserts:  a=5VCI|1|A|U|9 B=5VCI|1|B|U|4
    Insertion on left  5VCI|1|A|U|9
pMakeNodesProbeForInsertions:  a 5VCI|1|A|A|10 interacts with 5VCI|1|B|U|4
pMakeNodesProbeForInsertions:  B 5VCI|1|B|U|4 interacts with 5VCI|1|A|A|10
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5VCI|1|B|U|4 interacts with 5VCI|1|A|A|11
pMakeNodes probed for insert:  a=5VCI|1|A|A|10 B=5VCI|1|B|U|4
pMakeNodes making a cluster near strand break a=5VCI|1|A|A|10 B=5VCI|1|B|U|4
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 4 and then 5 to 5
aa is 4 bb is 5
  3 Cluster   5VCI|1|A|A|10:5VCI|1|A|A|11 5VCI|1|B|U|4:5VCI|1|B|U|4
    LR Inter  5VCI|1|A|A|10 5VCI|1|B|U|4 tSH 
    LR Inter  5VCI|1|A|A|11 5VCI|1|B|U|4 cWW 
    LL Inter  5VCI|1|A|A|10 5VCI|1|A|A|11 cSH 
pMakeNodesCluster a=5 B=4 at the end
pMakeNodesCluster a=5 B=4 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Cluster Left  3  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5VCI|1|A|U|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CU'
           RightLetter: 'G'
               Comment: ' // Basepair C8 - G5 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5VCI|1|A|U|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0146

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [3 4]
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AA'
           RightLetter: 'U'
               Comment: ' // Cluster node 5VCI|1|A|A|10:5VCI|1|A|A|11 and 5VCI|1|B|U|4:5VCI|1|B|U|4'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0146

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5   Cluster Left  3  4 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  4
pMakeMotifModelFromSSF:   7   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 7
pUpdateModelWithSSF: IL_14368.1 allow insertions from initial node 6?
ans =

    0.9912    0.0084    0.0004


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9912    0.0084    0.0004


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_14368.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.4141
   -2.4141
   -2.4141
   -2.4141
   -2.4141
  -10.1114

Timestamp 18-Jul-2025 22:46:54
pMakeSCFGModels: Making JAR3D model for motif group IL_14688.1, number 60 of 411
pMakeNodes starting loop:     a=8F4O|1|B|G|18 B=8F4O|1|B|C|48
  2 Basepair    18   48 GC cWW 
No need to probe because of interaction between a=8F4O|1|B|G|19 B=8F4O|1|B|A|47
  3 Basepair    19   47 GA cWW 
No need to probe because of interaction between a=8F4O|1|B|U|20 B=8F4O|1|B|A|45
  4 Basepair    20   45 UA cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G18 - C48 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G19 - A47 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U20 - A45 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_14688.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3837
   -6.3837
   -8.3858
   -6.0487
   -5.9729

Timestamp 18-Jul-2025 22:46:55
pMakeSCFGModels: Making JAR3D model for motif group IL_15052.4, number 61 of 411
pMakeNodes starting loop:     a=3MXH|1|R|A|61 B=3MXH|1|R|U|77
pMakeNodes making a cluster near strand break a=3MXH|1|R|A|61 B=3MXH|1|R|U|77
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 3 and then 6 to 6
aa is 3 bb is 6
  2 Cluster   3MXH|1|R|A|61:3MXH|1|R|A|63 3MXH|1|R|U|77:3MXH|1|R|U|77
    LR Inter  3MXH|1|R|A|61 3MXH|1|R|U|77 cWW 
    LR Inter  3MXH|1|R|A|63 3MXH|1|R|U|77 cWS 
    LL Inter  3MXH|1|R|A|61 3MXH|1|R|A|62 cSH 
pMakeNodesCluster a=4 B=5 at the end
pMakeNodesCluster a=4 B=5 at the end
No need to probe because of interaction between a=3MXH|1|R|C|64 B=3MXH|1|R|G|76
  3 Basepair    64   76 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 0 0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAA'
           RightLetter: 'U'
               Comment: ' // Cluster node 3MXH|1|R|A|61:3MXH|1|R|A|63 and 3MXH|1|R|U|77:3MXH|1|R|U|77'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0618
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C64 - G76 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  6
pMakeMotifModelFromSSF:   3   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_15052.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.0784
   -4.0784
   -4.4067
   -7.0039
   -4.1307
   -4.3207
   -4.3405
   -4.3405

Timestamp 18-Jul-2025 22:46:55
pMakeSCFGModels: Making JAR3D model for motif group IL_15107.1, number 62 of 411
pMakeNodes starting loop:     a=8D29|1|J|C|21 B=8D29|1|J|G|11
  2 Basepair    21   11 CG cWW 
pMakeNodes probe for inserts:  a=8D29|1|J|C|23 B=8D29|1|J|A|10
    Insertion on left  8D29|1|J|C|23
    Insertion on left  8D29|1|J|U|24
pMakeNodesProbeForInsertions:  a 8D29|1|J|U|25 interacts with 8D29|1|J|A|10
pMakeNodesProbeForInsertions:  B 8D29|1|J|A|10 interacts with 8D29|1|J|U|25
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8D29|1|J|A|10 interacts with 8D29|1|J|U|25
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8D29|1|J|U|25 B=8D29|1|J|A|10
  3 Basepair    25   10 UA cWW 
No need to probe because of interaction between a=8D29|1|J|G|26 B=8D29|1|J|C|9
  4 Basepair    26    9 GC cWW 
No need to probe because of interaction between a=8D29|1|J|G|27 B=8D29|1|J|C|8
  5 Basepair    27    8 GC cWW 
No need to probe because of interaction between a=8D29|1|J|C|28 B=8D29|1|J|A|7
  6 Basepair    28    7 CA bif 
No need to probe because of interaction between a=8D29|1|J|A|29 B=8D29|1|J|U|6
  7 Basepair    29    6 AU tHS 
No need to probe because of interaction between a=8D29|1|J|G|30 B=8D29|1|J|A|5
  8 Basepair    30    5 GA cWW 
No need to probe because of interaction between a=8D29|1|J|C|31 B=8D29|1|J|G|4
  9 Basepair    31    4 CG cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right 17
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right 16
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right 15
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right 14
pMakeMotifModelFromSSF:   7  Basepair Left  8 Right 13
pMakeMotifModelFromSSF:   8  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  10   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8D29|1|J|A|5
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8D29|1|J|U|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CCU'
           RightLetter: 'G'
               Comment: ' // Basepair C21 - G11 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8D29|1|J|A|5'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8D29|1|J|U|6'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U25 - A10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G26 - C9 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G27 - C8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C28 - A7 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A29 - U6 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G30 - A5 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C31 - G4 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 17
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 17
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 17
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 17
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right 17
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right 16
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right 15
pMakeMotifModelFromSSF:  10  Basepair Left  7 Right 14
pMakeMotifModelFromSSF:  11  Basepair Left  8 Right 13
pMakeMotifModelFromSSF:  12  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  13  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  14   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_15107.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.5141

Timestamp 18-Jul-2025 22:46:56
pMakeSCFGModels: Making JAR3D model for motif group IL_15218.1, number 63 of 411
pMakeNodes starting loop:     a=7QR3|1|C|C|7 B=7QR3|1|C|G|30
  2 Basepair     7   30 CG cWW 
pMakeNodes probe for inserts:  a=7QR3|1|C|A|8 B=7QR3|1|C|C|29
    Insertion on left  7QR3|1|C|A|8
    Insertion on left  7QR3|1|C|C|9
    Insertion on left  7QR3|1|C|A|10
    Insertion on left  7QR3|1|C|G|11
    Insertion on left  7QR3|1|C|C|12
    Insertion on left  7QR3|1|C|A|13
    Insertion on left  7QR3|1|C|G|14
    Insertion on left  7QR3|1|C|A|15
    Insertion on left  7QR3|1|C|A|16
pMakeNodesProbeForInsertions:  a 7QR3|1|C|G|17 interacts with 7QR3|1|C|C|29
pMakeNodesProbeForInsertions:  B 7QR3|1|C|C|29 interacts with 7QR3|1|C|G|17
pMakeNodesProbeForInsertions:  B 7QR3|1|C|C|29 interacts with 7QR3|1|C|G|17
pMakeNodes probed for insert:  a=7QR3|1|C|G|17 B=7QR3|1|C|C|29
  3 Basepair    17   29 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:   4   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR3|1|C|A|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR3|1|C|C|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR3|1|C|A|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR3|1|C|G|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR3|1|C|C|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR3|1|C|A|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR3|1|C|G|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR3|1|C|A|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR3|1|C|A|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-10 8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CACAGCAGAA'
           RightLetter: 'G'
               Comment: ' // Basepair C7 - G30 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR3|1|C|A|8'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR3|1|C|C|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR3|1|C|A|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR3|1|C|G|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR3|1|C|C|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR3|1|C|A|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR3|1|C|G|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR3|1|C|A|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR3|1|C|A|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G17 - C29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             LeftIndex: 12
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 12
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 12
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 12
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 12
pMakeMotifModelFromSSF:  18   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  19     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  20   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  21  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  22   Hairpin Left 12 Right 11
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Found a hairpin at node 22

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_15218.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.3814
  -10.3814

Timestamp 18-Jul-2025 22:46:56
pMakeSCFGModels: Making JAR3D model for motif group IL_15698.3, number 64 of 411
pMakeNodes starting loop:     a=5FJC|1|A|C|44 B=5FJC|1|A|G|58
  2 Basepair    44   58 CG cWW 
No need to probe because of interaction between a=5FJC|1|A|A|45 B=5FJC|1|A|U|57
  3 Basepair    45   57 AU tSH 
pMakeNodes probe for inserts:  a=5FJC|1|A|A|46 B=5FJC|1|A|G|56
pMakeNodesProbeForInsertions:  a 5FJC|1|A|A|46 interacts with 5FJC|1|A|C|47
pMakeNodesProbeForInsertions:  B 5FJC|1|A|G|56 interacts with 5FJC|1|A|C|47
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 5FJC|1|A|G|56 interacts with 5FJC|1|A|C|47
pMakeNodes probed for insert:  a=5FJC|1|A|A|46 B=5FJC|1|A|G|56
pMakeNodes making a cluster near strand break a=5FJC|1|A|A|46 B=5FJC|1|A|G|56
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 4 and then 5 to 5
aa is 4 bb is 5
  4 Cluster   5FJC|1|A|A|46:5FJC|1|A|C|47 5FJC|1|A|G|56:5FJC|1|A|G|56
    LR Inter  5FJC|1|A|C|47 5FJC|1|A|G|56 cWW 
    LL Inter  5FJC|1|A|A|46 5FJC|1|A|C|47 cSH 
pMakeNodesCluster a=5 B=4 at the end
pMakeNodesCluster a=5 B=4 at the end
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Cluster Left  3  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C44 - G58 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A45 - U57 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4]
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AC'
           RightLetter: 'G'
               Comment: ' // Cluster node 5FJC|1|A|A|46:5FJC|1|A|C|47 and 5FJC|1|A|G|56:5FJC|1|A|G|56'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2506

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Cluster Left  3  4 Right  5
pMakeMotifModelFromSSF:   5   Initial Left  5 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pUpdateModelWithSSF: IL_15698.3 allow insertions from initial node 5?
ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_15698.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.4830
   -4.4830
   -4.4830
   -4.4830
   -4.4830
   -6.1310
   -7.5685
   -6.1310
  -11.4536
   -7.5685

Timestamp 18-Jul-2025 22:46:56
pMakeSCFGModels: Making JAR3D model for motif group IL_15991.1, number 65 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|G|669 B=8CRE|1|CM|C|656
  2 Basepair   669  656 GC cWW 
pMakeNodes probe for inserts:  a=8CRE|1|CM|G|671 B=8CRE|1|CM|U|655
    Insertion on left  8CRE|1|CM|G|671
    Insertion on left  8CRE|1|CM|U|672
    Insertion on left  8CRE|1|CM|A|673
    Insertion on left  8CRE|1|CM|C|674
    Insertion on left  8CRE|1|CM|U|675
    Insertion on left  8CRE|1|CM|G|676
    Insertion on left  8CRE|1|CM|G|677
    Insertion on left  8CRE|1|CM|A|678
    Insertion on left  8CRE|1|CM|C|680
    Insertion on left  8CRE|1|CM|C|681
    Insertion on right 8CRE|1|CM|U|655
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|A|682 interacts with 8CRE|1|CM|U|648
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|654 interacts with 8CRE|1|CM|G|653
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|654 interacts with 8CRE|1|CM|G|653
pMakeNodes probed for insert:  a=8CRE|1|CM|A|682 B=8CRE|1|CM|G|654
pMakeNodes making a cluster near strand break a=8CRE|1|CM|A|682 B=8CRE|1|CM|G|654
pMakeNodesCluster: amax is 12 bmin is 13, use_amax is 1
pMakeNodesCluster: Cluster goes from 12 to 12 and then 13 to 19
aa is 12 bb is 13
  3 Cluster   8CRE|1|CM|A|682:8CRE|1|CM|A|682 8CRE|1|CM|U|648:8CRE|1|CM|G|654
    LR Inter  8CRE|1|CM|A|682 8CRE|1|CM|U|648 cWW 
    RR Inter  8CRE|1|CM|G|653 8CRE|1|CM|G|654 cSH 
    Right strand conserved insertion 8CRE|1|CM|G|649 at position 2
    Right strand conserved insertion 8CRE|1|CM|G|650 at position 3
    Right strand conserved insertion 8CRE|1|CM|C|651 at position 4
    Right strand conserved insertion 8CRE|1|CM|C|652 at position 5
pMakeNodesCluster a=13 B=12 at the end
pMakeNodesCluster a=13 B=12 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 21
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 21
pMakeMotifModelFromSSF:   3   Cluster Left 12 Right 13 14 15 16 17 18 19
pMakeMotifModelFromSSF:   4   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|G|649
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|G|650
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|C|651
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|C|652
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|G|653
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|G|654
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|U|655
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|C|656
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|G|669
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|C|670
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|CM|C|679
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 21
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [21×21 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-11 8.1893e-10 8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 … ]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGUACUGGACC'
           RightLetter: 'UC'
               Comment: ' // Basepair G669 - C656 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|G|649'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2 3 4 5 6 7]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [2 3 4 5]
              NormCons: 1.0000

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|G|650'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|C|651'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|C|652'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|G|653'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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                  rpar: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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          InterIndices: []
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                  rpar: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|G|654'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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               subtype: []
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                  rpar: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                  rpar: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|U|655'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                  rpar: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|C|656'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
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                  rpar: []
          LeftNotInter: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|G|669'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 11
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             LeftIndex: 11
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|C|670'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 12
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             LeftIndex: 12
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|CM|C|679'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 12
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 26
             LeftIndex: 12
            RightIndex: [13 14 15 16 17 18 19]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: 'UGGCCGG'
               Comment: ' // Cluster node 8CRE|1|CM|A|682:8CRE|1|CM|A|682 and 8CRE|1|CM|U|648:8CRE|1|CM|G|654'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2 3 4 5 6 7]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [2 3 4 5]
              NormCons: 1.0000

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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         RightNotInter: []
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Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 29
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 21
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 21
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 20
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 20
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 20
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 20
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 20
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 20
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 20
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 20
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 20
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 20
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 20
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 20
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 20
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 20
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 20
pMakeMotifModelFromSSF:  18   Initial Left 10 Right 20
pMakeMotifModelFromSSF:  19     Fixed Left 10 Right 20
pMakeMotifModelFromSSF:  20   Initial Left 11 Right 20
pMakeMotifModelFromSSF:  21     Fixed Left 11 Right 20
pMakeMotifModelFromSSF:  22   Initial Left 12 Right 20
pMakeMotifModelFromSSF:  23     Fixed Left 12 Right 20
pMakeMotifModelFromSSF:  24   Initial Left 12 Right 19
pMakeMotifModelFromSSF:  25   Cluster Left 12 Right 13 14 15 16 17 18 19
pMakeMotifModelFromSSF:  26   Initial Left 13 Right 12
pMakeMotifModelFromSSF:  27   Hairpin Left 13 Right 12
pNextNodeJunction: Found a hairpin at node 27
pUpdateModelWithSSF: IL_15991.1 allow insertions from initial node 26?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 27

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_15991.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -16.4481

Timestamp 18-Jul-2025 22:46:57
pMakeSCFGModels: Making JAR3D model for motif group IL_16218.2, number 66 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|G|1250 B=8P9A|1|AR|C|1238
  2 Basepair  1250 1238 GC cWW 
No need to probe because of interaction between a=8P9A|1|AR|A|1251 B=8P9A|1|AR|G|1237
  3 Basepair  1251 1237 AG cWW 
pMakeNodes probe for inserts:  a=8P9A|1|AR|A|1252 B=8P9A|1|AR|U|1235
    Insertion on left  8P9A|1|AR|A|1252
    Insertion on left  8P9A|1|AR|U|1253
    Insertion on right 8P9A|1|AR|U|1235
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|C|1254 interacts with 8P9A|1|AR|G|1234
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|G|1234 interacts with 8P9A|1|AR|C|1254
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|G|1234 interacts with 8P9A|1|AR|C|1254
pMakeNodes probed for insert:  a=8P9A|1|AR|C|1254 B=8P9A|1|AR|G|1234
  4 Basepair  1254 1234 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|G|1236
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|G|1237
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|A|1251
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1250 - C1238 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAU'
           RightLetter: 'UG'
               Comment: ' // Basepair A1251 - G1237 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|G|1236'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|G|1237'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|A|1251'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1254 - G1234 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_16218.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3399
   -6.3399
   -7.9257

Timestamp 18-Jul-2025 22:46:57
pMakeSCFGModels: Making JAR3D model for motif group IL_16386.4, number 67 of 411
pMakeNodes starting loop:     a=8GXB|1|A|C|40 B=8GXB|1|A|G|6
  2 Basepair    40    6 CG cWW 
pMakeNodes probe for inserts:  a=8GXB|1|A|G|41 B=8GXB|1|A|C|5
    Insertion on left  8GXB|1|A|G|41
pMakeNodesProbeForInsertions:  a 8GXB|1|A|G|42 interacts with 8GXB|1|A|C|5
pMakeNodesProbeForInsertions:  B 8GXB|1|A|C|5 interacts with 8GXB|1|A|G|42
pMakeNodesProbeForInsertions:  B 8GXB|1|A|C|5 interacts with 8GXB|1|A|G|42
pMakeNodes probed for insert:  a=8GXB|1|A|G|42 B=8GXB|1|A|C|5
  3 Basepair    42    5 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8GXB|1|A|G|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CG'
           RightLetter: 'G'
               Comment: ' // Basepair C40 - G6 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8GXB|1|A|G|6'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G42 - C5 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_16386.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.1313
   -3.1313
   -3.1313
   -3.1313

Timestamp 18-Jul-2025 22:46:58
pMakeSCFGModels: Making JAR3D model for motif group IL_16458.4, number 68 of 411
pMakeNodes starting loop:     a=7A0S|1|X|C|2631 B=7A0S|1|X|G|2647
  2 Basepair  2631 2647 CG cWW 
pMakeNodes probe for inserts:  a=7A0S|1|X|U|2632 B=7A0S|1|X|C|2646
    Insertion on left  7A0S|1|X|U|2632
    Insertion on left  7A0S|1|X|A|2633
    Insertion on right 7A0S|1|X|C|2646
    Insertion on right 7A0S|1|X|C|2645
pMakeNodesProbeForInsertions:  a 7A0S|1|X|G|2634 interacts with 7A0S|1|X|U|2635
pMakeNodesProbeForInsertions:  B 7A0S|1|X|A|2644 interacts with 7A0S|1|X|U|2635
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 7A0S|1|X|A|2644 interacts with 7A0S|1|X|U|2635
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=7A0S|1|X|G|2634 B=7A0S|1|X|A|2644
pMakeNodes making a cluster near strand break a=7A0S|1|X|G|2634 B=7A0S|1|X|A|2644
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 10 to 10
aa is 5 bb is 10
  3 Cluster   7A0S|1|X|G|2634:7A0S|1|X|U|2635 7A0S|1|X|A|2644:7A0S|1|X|A|2644
    LR Inter  7A0S|1|X|U|2635 7A0S|1|X|A|2644 tWH 
    LL Inter  7A0S|1|X|G|2634 7A0S|1|X|U|2635 cSH 
pMakeNodesCluster a=6 B=9 at the end
pMakeNodesCluster a=6 B=9 at the end
No need to probe because of interaction between a=7A0S|1|X|A|2636 B=7A0S|1|X|G|2643
  4 Basepair  2636 2643 AG tHS 
No need to probe because of interaction between a=7A0S|1|X|C|2637 B=7A0S|1|X|G|2642
  5 Basepair  2637 2642 CG cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  4  5 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|U|2632
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|A|2633
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|C|2646
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7A0S|1|X|C|2645
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CUA'
           RightLetter: 'CCG'
               Comment: ' // Basepair C2631 - G2647 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7A0S|1|X|U|2632'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7A0S|1|X|A|2633'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7A0S|1|X|C|2646'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7A0S|1|X|C|2645'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 12
             LeftIndex: [4 5]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 7A0S|1|X|G|2634:7A0S|1|X|U|2635 and 7A0S|1|X|A|2644:7A0S|1|X|A|2644'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A2636 - G2643 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2637 - G2642 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  4 Right 10
pMakeMotifModelFromSSF:  11   Cluster Left  4  5 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  15   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a hairpin at node 15

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_16458.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.5673
   -4.5673
   -4.5673
   -5.3591
   -7.2250

Timestamp 18-Jul-2025 22:46:58
pMakeSCFGModels: Making JAR3D model for motif group IL_16665.1, number 69 of 411
pMakeNodes starting loop:     a=5KPY|1|A|G|47 B=5KPY|1|A|C|75
  2 Basepair    47   75 GC cWW 
pMakeNodes probe for inserts:  a=5KPY|1|A|A|48 B=5KPY|1|A|A|74
    Insertion on left  5KPY|1|A|A|48
    Insertion on left  5KPY|1|A|U|51
    Insertion on left  5KPY|1|A|G|52
    Insertion on left  5KPY|1|A|U|54
    Insertion on right 5KPY|1|A|A|74
    Insertion on right 5KPY|1|A|A|73
    Insertion on right 5KPY|1|A|U|72
pMakeNodesProbeForInsertions:  a 5KPY|1|A|G|55 interacts with 5KPY|1|A|C|71
pMakeNodesProbeForInsertions:  B 5KPY|1|A|C|71 interacts with 5KPY|1|A|G|55
pMakeNodesProbeForInsertions:  B 5KPY|1|A|C|71 interacts with 5KPY|1|A|G|55
pMakeNodes probed for insert:  a=5KPY|1|A|G|55 B=5KPY|1|A|C|71
  3 Basepair    55   71 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5KPY|1|A|A|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5KPY|1|A|A|49
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5KPY|1|A|U|50
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5KPY|1|A|U|51
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5KPY|1|A|C|71
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5KPY|1|A|G|55
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5KPY|1|A|U|54
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAUGU'
           RightLetter: 'UAAC'
               Comment: ' // Basepair G47 - C75 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5KPY|1|A|A|48'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5KPY|1|A|A|49'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5KPY|1|A|U|50'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5KPY|1|A|U|51'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5KPY|1|A|C|71'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5KPY|1|A|G|55'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5KPY|1|A|U|54'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G55 - C71 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 20
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  13     Fixed Left  6 Right  9
pMakeMotifModelFromSSF:  14   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  15     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  16   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  17  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  18   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a hairpin at node 18

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_16665.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.3767

Timestamp 18-Jul-2025 22:46:58
pMakeSCFGModels: Making JAR3D model for motif group IL_17069.5, number 70 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|G|1813 B=5J7L|1|DA|C|1804
  2 Basepair  1813 1804 GC cWW 
No need to probe because of interaction between a=5J7L|1|DA|G|1814 B=5J7L|1|DA|A|1803
  3 Basepair  1814 1803 GA tSH 
No need to probe because of interaction between a=5J7L|1|DA|A|1815 B=5J7L|1|DA|A|1802
pMakeNodes making a cluster near strand break a=5J7L|1|DA|A|1815 B=5J7L|1|DA|A|1802
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 7 and then 8 to 11
aa is 7 bb is 8
  4 Cluster   5J7L|1|DA|A|1815:5J7L|1|DA|A|1821 5J7L|1|DA|U|1798:5J7L|1|DA|A|1802
    LR Inter  5J7L|1|DA|A|1821 5J7L|1|DA|U|1798 cWW 
    LR Inter  5J7L|1|DA|U|1818 5J7L|1|DA|G|1799 tSS 
    LR Inter  5J7L|1|DA|G|1817 5J7L|1|DA|C|1800 tWW 
    LR Inter  5J7L|1|DA|A|1819 5J7L|1|DA|C|1800 tHH 
    LR Inter  5J7L|1|DA|A|1815 5J7L|1|DA|A|1802 tHH 
    RR Inter  5J7L|1|DA|U|1798 5J7L|1|DA|A|1802 cSS 
pMakeNodesCluster a=8 B=7 at the end
pMakeNodesCluster a=8 B=7 at the end
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6  7 Right  8  9 10 11
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1813 - C1804 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1814 - A1803 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4 5 6 7]
            RightIndex: [8 9 10 11]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGUAA'
           RightLetter: 'UGCA'
               Comment: ' // Cluster node 5J7L|1|DA|A|1815:5J7L|1|DA|A|1821 and 5J7L|1|DA|U|1798:5J7L|1|DA|A|1802'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0224

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6  7 Right  8  9 10 11
pMakeMotifModelFromSSF:   5   Initial Left  8 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 6
pUpdateModelWithSSF: IL_17069.5 allow insertions from initial node 5?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_17069.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.7917
   -9.1498
   -8.3025
   -9.2578
  -12.7005

Timestamp 18-Jul-2025 22:46:59
pMakeSCFGModels: Making JAR3D model for motif group IL_17136.7, number 71 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|C|975 B=8CRE|1|CM|G|999
  2 Basepair   975  999 CG cWW 
No need to probe because of interaction between a=8CRE|1|CM|G|976 B=8CRE|1|CM|A|998
  3 Basepair   976  998 GA tSH 
No need to probe because of interaction between a=8CRE|1|CM|A|977 B=8CRE|1|CM|U|997
  4 Basepair   977  997 AU tHW 
No need to probe because of interaction between a=8CRE|1|CM|A|978 B=8CRE|1|CM|G|996
  5 Basepair   978  996 AG tHS 
No need to probe because of interaction between a=8CRE|1|CM|G|979 B=8CRE|1|CM|C|995
  6 Basepair   979  995 GC cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C975 - G999 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G976 - A998 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A977 - U997 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A978 - G996 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G979 - C995 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_17136.7_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7435
   -6.7435
   -7.8046
   -7.8046
   -6.7737
   -6.7737
   -7.6569
   -7.6516
   -6.0194
   -6.4991
   -7.3327
   -7.6213
   -6.2638
   -7.1416

Timestamp 18-Jul-2025 22:47:00
pMakeSCFGModels: Making JAR3D model for motif group IL_17765.1, number 72 of 411
pMakeNodes starting loop:     a=3D2V|1|A|C|26 B=3D2V|1|A|G|13
  2 Basepair    26   13 CG cWW 
pMakeNodes probe for inserts:  a=3D2V|1|A|U|27 B=3D2V|1|A|U|12
pMakeNodesProbeForInsertions:  a 3D2V|1|A|U|27 interacts with 3D2V|1|A|A|31
pMakeNodesProbeForInsertions:  B 3D2V|1|A|U|12 interacts with 3D2V|1|A|A|33
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 3D2V|1|A|U|12 interacts with 3D2V|1|A|A|33
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3D2V|1|A|U|27 B=3D2V|1|A|U|12
pMakeNodes making a cluster near strand break a=3D2V|1|A|U|27 B=3D2V|1|A|U|12
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 10 and then 11 to 13
aa is 10 bb is 11
  3 Cluster   3D2V|1|A|U|27:3D2V|1|A|C|36 3D2V|1|A|G|10:3D2V|1|A|U|12
    LR Inter  3D2V|1|A|C|36 3D2V|1|A|G|10 cWW 
    LR Inter  3D2V|1|A|G|30 3D2V|1|A|G|11 tSS 
    LR Inter  3D2V|1|A|G|34 3D2V|1|A|G|11 cHW 
    LR Inter  3D2V|1|A|A|33 3D2V|1|A|U|12 cHW 
    LL Inter  3D2V|1|A|U|27 3D2V|1|A|A|31 tWH 
    LL Inter  3D2V|1|A|A|29 3D2V|1|A|C|36 cSS 
    Left  strand conserved insertion 3D2V|1|A|G|28 at position 2
    Left  strand conserved insertion 3D2V|1|A|A|32 at position 6
pMakeNodesCluster a=11 B=10 at the end
pMakeNodesCluster a=11 B=10 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8  9 10 Right 11 12 13
pMakeMotifModelFromSSF:   4   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 0 0 0 0 0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C26 - G13 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5 6 7 8 9 10]
            RightIndex: [11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGAGAAAGC'
           RightLetter: 'GGU'
               Comment: ' // Cluster node 3D2V|1|A|U|27:3D2V|1|A|C|36 and 3D2V|1|A|G|10:3D2V|1|A|U|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8 9]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 6]
         RightNotInter: [1×0 double]
              NormCons: 0.1009

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8  9 10 Right 11 12 13
pMakeMotifModelFromSSF:   4   Initial Left 11 Right 10
pMakeMotifModelFromSSF:   5   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_17765.1 allow insertions from initial node 4?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_17765.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3880

Timestamp 18-Jul-2025 22:47:00
pMakeSCFGModels: Making JAR3D model for motif group IL_17948.2, number 73 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|2466 B=5J7L|1|DA|G|2484
  2 Basepair  2466 2484 CG cWW 
No need to probe because of interaction between a=5J7L|1|DA|C|2467 B=5J7L|1|DA|C|2483
  3 Basepair  2467 2483 CC bif 
No need to probe because of interaction between a=5J7L|1|DA|A|2468 B=5J7L|1|DA|A|2482
  4 Basepair  2468 2482 AA tSH 
No need to probe because of interaction between a=5J7L|1|DA|A|2469 B=5J7L|1|DA|G|2481
  5 Basepair  2469 2481 AG tHS 
No need to probe because of interaction between a=5J7L|1|DA|G|2470 B=5J7L|1|DA|C|2480
  6 Basepair  2470 2480 GC cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2466 - G2484 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C2467 - C2483 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A2468 - A2482 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A2469 - G2481 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2470 - C2480 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_17948.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4166
   -6.5078
   -6.5078
   -6.4166
   -7.2468
   -7.2468
   -7.0260
   -6.4597
   -6.8206
   -8.7309
   -6.4597
  -10.4852
  -18.2694

Timestamp 18-Jul-2025 22:47:01
pMakeSCFGModels: Making JAR3D model for motif group IL_17973.1, number 74 of 411
pMakeNodes starting loop:     a=6UFG|1|A|C|116 B=6UFG|1|A|G|99
  2 Basepair   116   99 CG cWW 
No need to probe because of interaction between a=6UFG|1|A|A|117 B=6UFG|1|A|G|98
  3 Basepair   117   98 AG cWW 
pMakeNodes probe for inserts:  a=6UFG|1|A|A|118 B=6UFG|1|A|G|96
    Insertion on left  6UFG|1|A|A|118
    Insertion on left  6UFG|1|A|G|119
    Insertion on left  6UFG|1|A|C|120
    Insertion on left  6UFG|1|A|G|121
    Insertion on left  6UFG|1|A|G|122
    Insertion on left  6UFG|1|A|G|123
    Insertion on left  6UFG|1|A|G|124
    Insertion on left  6UFG|1|A|U|125
    Insertion on left  6UFG|1|A|G|126
    Insertion on left  6UFG|1|A|G|127
    Insertion on left  6UFG|1|A|C|128
    Insertion on left  6UFG|1|A|C|130
pMakeNodesProbeForInsertions:  a 6UFG|1|A|C|131 interacts with 6UFG|1|A|G|96
pMakeNodesProbeForInsertions:  B 6UFG|1|A|G|96 interacts with 6UFG|1|A|C|131
pMakeNodesProbeForInsertions:  B 6UFG|1|A|G|96 interacts with 6UFG|1|A|C|131
pMakeNodes probed for insert:  a=6UFG|1|A|C|131 B=6UFG|1|A|G|96
  4 Basepair   131   96 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:   5   Hairpin Left 16 Right 15
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|G|98
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|G|99
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|C|116
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|A|117
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|A|118
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|G|119
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|C|120
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|G|121
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|G|122
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|G|123
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|G|124
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|U|125
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C116 - G99 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-13 8.1893e-12 8.1893e-11 8.1893e-10 8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 … ]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAGCGGGGUGGCC'
           RightLetter: 'G'
               Comment: ' // Basepair A117 - G98 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|G|98'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 16
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|G|99'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|C|116'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|A|117'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|A|118'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|G|119'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                IBases: []
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                  lpar: []
                  rpar: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|C|120'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 10
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|G|121'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 11
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             LeftIndex: 11
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|G|122'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             LeftIndex: 12
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 23
             LeftIndex: 12
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|G|123'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 13
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 25
             LeftIndex: 13
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|G|124'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 26
             LeftIndex: 14
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 27
             LeftIndex: 14
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|U|125'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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                  lpar: []
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Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 28
             LeftIndex: 15
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                  lpar: []
                  rpar: []
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Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 29
             LeftIndex: 15
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C131 - G96 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 29

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 31
             LeftIndex: 16
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 16
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 16
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 16
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 16
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 16
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 16
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 16
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 16
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 16
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 16
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 16
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 16
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 16
pMakeMotifModelFromSSF:  16     Fixed Left  9 Right 16
pMakeMotifModelFromSSF:  17   Initial Left 10 Right 16
pMakeMotifModelFromSSF:  18     Fixed Left 10 Right 16
pMakeMotifModelFromSSF:  19   Initial Left 11 Right 16
pMakeMotifModelFromSSF:  20     Fixed Left 11 Right 16
pMakeMotifModelFromSSF:  21   Initial Left 12 Right 16
pMakeMotifModelFromSSF:  22     Fixed Left 12 Right 16
pMakeMotifModelFromSSF:  23   Initial Left 13 Right 16
pMakeMotifModelFromSSF:  24     Fixed Left 13 Right 16
pMakeMotifModelFromSSF:  25   Initial Left 14 Right 16
pMakeMotifModelFromSSF:  26     Fixed Left 14 Right 16
pMakeMotifModelFromSSF:  27   Initial Left 15 Right 16
pMakeMotifModelFromSSF:  28  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  29   Hairpin Left 16 Right 15
pNextNodeJunction: Found a hairpin at node 29
pNextNodeJunction: Found a hairpin at node 29

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_17973.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -14.1073

Timestamp 18-Jul-2025 22:47:02
pMakeSCFGModels: Making JAR3D model for motif group IL_18354.1, number 75 of 411
pMakeNodes starting loop:     a=3NPQ|1|A|G|7 B=3NPQ|1|A|C|32
  2 Basepair     7   32 GC cWW 
pMakeNodes probe for inserts:  a=3NPQ|1|A|G|8 B=3NPQ|1|A|G|31
    Insertion on left  3NPQ|1|A|G|8
    Insertion on left  3NPQ|1|A|A|9
    Insertion on left  3NPQ|1|A|G|10
    Insertion on left  3NPQ|1|A|C|11
    Insertion on left  3NPQ|1|A|G|12
    Insertion on left  3NPQ|1|A|C|13
    Insertion on left  3NPQ|1|A|U|14
    Insertion on left  3NPQ|1|A|G|15
pMakeNodesProbeForInsertions:  a 3NPQ|1|A|C|16 interacts with 3NPQ|1|A|G|31
pMakeNodesProbeForInsertions:  B 3NPQ|1|A|G|31 interacts with 3NPQ|1|A|C|16
pMakeNodesProbeForInsertions:  B 3NPQ|1|A|G|31 interacts with 3NPQ|1|A|C|16
pMakeNodes probed for insert:  a=3NPQ|1|A|C|16 B=3NPQ|1|A|G|31
  3 Basepair    16   31 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   4   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|G|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|A|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|G|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|C|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|G|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|C|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|U|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|G|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGAGCGCUG'
           RightLetter: 'C'
               Comment: ' // Basepair G7 - C32 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|G|8'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|A|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|G|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|C|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|G|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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                  lpar: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|C|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|U|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|G|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C16 - G31 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 22
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 11
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  18   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  19  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  20   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Found a hairpin at node 20

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_18354.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.7345
  -11.4280

Timestamp 18-Jul-2025 22:47:02
pMakeSCFGModels: Making JAR3D model for motif group IL_18472.4, number 76 of 411
pMakeNodes starting loop:     a=5J7L|1|DB|G|23 B=5J7L|1|DB|C|60
  2 Basepair    23   60 GC cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DB|G|24 B=5J7L|1|DB|A|59
    Insertion on right 5J7L|1|DB|A|59
    Insertion on right 5J7L|1|DB|A|58
    Insertion on right 5J7L|1|DB|A|57
pMakeNodesProbeForInsertions:  a 5J7L|1|DB|G|24 interacts with 5J7L|1|DB|C|27
pMakeNodesProbeForInsertions:  B 5J7L|1|DB|G|56 interacts with 5J7L|1|DB|C|28
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 5J7L|1|DB|G|56 interacts with 5J7L|1|DB|C|28
pMakeNodes probed for insert:  a=5J7L|1|DB|G|24 B=5J7L|1|DB|G|56
pMakeNodes making a cluster near strand break a=5J7L|1|DB|G|24 B=5J7L|1|DB|G|56
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 6 and then 7 to 7
aa is 6 bb is 7
  3 Cluster   5J7L|1|DB|G|24:5J7L|1|DB|C|28 5J7L|1|DB|G|56:5J7L|1|DB|G|56
    LR Inter  5J7L|1|DB|C|28 5J7L|1|DB|G|56 cWW 
    LL Inter  5J7L|1|DB|G|24 5J7L|1|DB|C|27 tSW 
    Left  strand conserved insertion 5J7L|1|DB|U|25 at position 2
    Left  strand conserved insertion 5J7L|1|DB|C|26 at position 3
pMakeNodesCluster a=7 B=6 at the end
pMakeNodesCluster a=7 B=6 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DB|A|59
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DB|A|58
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DB|A|57
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'AAAC'
               Comment: ' // Basepair G23 - C60 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DB|A|59'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DB|A|58'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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                 Right: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DB|A|57'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 10
             LeftIndex: [2 3 4 5 6]
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUCCC'
           RightLetter: 'G'
               Comment: ' // Cluster node 5J7L|1|DB|G|24:5J7L|1|DB|C|28 and 5J7L|1|DB|G|56:5J7L|1|DB|G|56'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  2 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  2 Right  7
pMakeMotifModelFromSSF:   9   Cluster Left  2  3  4  5  6 Right  7
pMakeMotifModelFromSSF:  10   Initial Left  7 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 11
pUpdateModelWithSSF: IL_18472.4 allow insertions from initial node 10?
ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_18472.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.6035
   -5.4461
   -5.4461

Timestamp 18-Jul-2025 22:47:02
pMakeSCFGModels: Making JAR3D model for motif group IL_18487.1, number 77 of 411
pMakeNodes starting loop:     a=8P9A|1|AS|G|21 B=8P9A|1|AS|C|58
  2 Basepair    21   58 GC cWW 
pMakeNodes probe for inserts:  a=8P9A|1|AS|A|22 B=8P9A|1|AS|G|57
    Insertion on left  8P9A|1|AS|A|22
    Insertion on left  8P9A|1|AS|A|23
    Insertion on left  8P9A|1|AS|A|24
    Insertion on left  8P9A|1|AS|G|25
    Insertion on right 8P9A|1|AS|G|57
pMakeNodesProbeForInsertions:  a 8P9A|1|AS|C|26 interacts with 8P9A|1|AS|U|54
pMakeNodesProbeForInsertions:  B 8P9A|1|AS|A|56 interacts with 8P9A|1|AS|A|27
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8P9A|1|AS|A|56 interacts with 8P9A|1|AS|U|54
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|AS|C|26 B=8P9A|1|AS|A|56
pMakeNodes making a cluster near strand break a=8P9A|1|AS|C|26 B=8P9A|1|AS|A|56
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 6 to 7 and then 8 to 11
aa is 7 bb is 8
  3 Cluster   8P9A|1|AS|C|26:8P9A|1|AS|A|27 8P9A|1|AS|U|53:8P9A|1|AS|A|56
    LR Inter  8P9A|1|AS|A|27 8P9A|1|AS|U|53 cWW 
    LR Inter  8P9A|1|AS|C|26 8P9A|1|AS|U|54 cWW 
    LR Inter  8P9A|1|AS|A|27 8P9A|1|AS|A|56 cSW 
    RR Inter  8P9A|1|AS|U|54 8P9A|1|AS|A|56 cSH 
    Right strand conserved insertion 8P9A|1|AS|A|55 at position 3
pMakeNodesCluster a=8 B=7 at the end
pMakeNodesCluster a=8 B=7 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  6  7 Right  8  9 10 11
pMakeMotifModelFromSSF:   4   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AS|A|22
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AS|A|23
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AS|A|24
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AS|G|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AS|G|57
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAAAG'
           RightLetter: 'GC'
               Comment: ' // Basepair G21 - C58 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AS|A|22'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: 3
              NormCons: 0.0244

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AS|A|23'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AS|A|24'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AS|G|25'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AS|G|57'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 14
             LeftIndex: [6 7]
            RightIndex: [8 9 10 11]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CA'
           RightLetter: 'UUAA'
               Comment: ' // Cluster node 8P9A|1|AS|C|26:8P9A|1|AS|A|27 and 8P9A|1|AS|U|53:8P9A|1|AS|A|56'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: 3
              NormCons: 0.0244

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  13   Cluster Left  6  7 Right  8  9 10 11
pMakeMotifModelFromSSF:  14   Initial Left  8 Right  7
pMakeMotifModelFromSSF:  15   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 15
pUpdateModelWithSSF: IL_18487.1 allow insertions from initial node 14?
ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 15

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_18487.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.6423
   -5.6423

Timestamp 18-Jul-2025 22:47:03
pMakeSCFGModels: Making JAR3D model for motif group IL_19048.1, number 78 of 411
pMakeNodes starting loop:     a=4WF9|1|Y|A|20 B=4WF9|1|Y|U|59
  2 Basepair    20   59 AU cWW 
No need to probe because of interaction between a=4WF9|1|Y|G|21 B=4WF9|1|Y|G|58
  3 Basepair    21   58 GG bif 
No need to probe because of interaction between a=4WF9|1|Y|G|22 B=4WF9|1|Y|G|57
pMakeNodes making a cluster near strand break a=4WF9|1|Y|G|22 B=4WF9|1|Y|G|57
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 6 and then 9 to 12
aa is 6 bb is 9
  4 Cluster   4WF9|1|Y|G|22:4WF9|1|Y|C|26 4WF9|1|Y|U|54:4WF9|1|Y|G|57
    LR Inter  4WF9|1|Y|C|26 4WF9|1|Y|U|54 cWW 
    LR Inter  4WF9|1|Y|G|22 4WF9|1|Y|G|57 bif 
    LR Inter  4WF9|1|Y|C|26 4WF9|1|Y|G|57 cSW 
    RR Inter  4WF9|1|Y|U|54 4WF9|1|Y|A|56 cSH 
    Left  strand conserved insertion 4WF9|1|Y|C|24 at position 2
    Left  strand conserved insertion 4WF9|1|Y|A|25 at position 3
    Right strand conserved insertion 4WF9|1|Y|A|55 at position 2
pMakeNodesCluster a=7 B=8 at the end
pMakeNodesCluster a=7 B=8 at the end
No need to probe because of interaction between a=4WF9|1|Y|A|27 B=4WF9|1|Y|U|53
  5 Basepair    27   53 AU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6 Right  9 10 11 12
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A20 - U59 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G21 - G58 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4 5 6]
            RightIndex: [9 10 11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCAC'
           RightLetter: 'UAAG'
               Comment: ' // Cluster node 4WF9|1|Y|G|22:4WF9|1|Y|C|26 and 4WF9|1|Y|U|54:4WF9|1|Y|G|57'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3]
         RightNotInter: 2
              NormCons: 0.0380

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A27 - U53 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6 Right  9 10 11 12
pMakeMotifModelFromSSF:   5   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_19048.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.1859

Timestamp 18-Jul-2025 22:47:03
pMakeSCFGModels: Making JAR3D model for motif group IL_19102.1, number 79 of 411
pMakeNodes starting loop:     a=4PMI|1|A|U|41 B=4PMI|1|A|G|77
  2 Basepair    41   77 UG cWW 
pMakeNodes probe for inserts:  a=4PMI|1|A|A|42 B=4PMI|1|A|G|76
    Insertion on left  4PMI|1|A|A|42
pMakeNodesProbeForInsertions:  a 4PMI|1|A|A|44 interacts with 4PMI|1|A|G|76
pMakeNodesProbeForInsertions:  B 4PMI|1|A|G|76 interacts with 4PMI|1|A|A|44
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4PMI|1|A|G|76 interacts with 4PMI|1|A|A|44
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4PMI|1|A|A|44 B=4PMI|1|A|G|76
  3 Basepair    44   76 AG cWW 
No need to probe because of interaction between a=4PMI|1|A|U|45 B=4PMI|1|A|A|75
  4 Basepair    45   75 UA cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4PMI|1|A|A|42
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: 'G'
               Comment: ' // Basepair U41 - G77 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4PMI|1|A|A|42'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A44 - G76 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U45 - A75 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_19102.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3604
   -7.6734

Timestamp 18-Jul-2025 22:47:04
pMakeSCFGModels: Making JAR3D model for motif group IL_19516.1, number 80 of 411
pMakeNodes starting loop:     a=8T29|1|R|G|17 B=8T29|1|R|C|50
  2 Basepair    17   50 GC cWW 
pMakeNodes probe for inserts:  a=8T29|1|R|G|19 B=8T29|1|R|A|49
    Insertion on left  8T29|1|R|G|19
    Insertion on left  8T29|1|R|G|20
    Insertion on left  8T29|1|R|A|21
    Insertion on left  8T29|1|R|C|22
    Insertion on left  8T29|1|R|C|23
    Insertion on left  8T29|1|R|U|24
    Insertion on left  8T29|1|R|A|25
    Insertion on left  8T29|1|R|C|26
    Insertion on left  8T29|1|R|C|27
    Insertion on left  8T29|1|R|C|28
    Insertion on right 8T29|1|R|A|49
    Insertion on right 8T29|1|R|A|48
pMakeNodesProbeForInsertions:  a 8T29|1|R|A|29 interacts with 8T29|1|R|G|47
pMakeNodesProbeForInsertions:  B 8T29|1|R|G|47 interacts with 8T29|1|R|A|29
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8T29|1|R|G|47 interacts with 8T29|1|R|A|29
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8T29|1|R|A|29 B=8T29|1|R|G|47
  3 Basepair    29   47 AG cWW 
No need to probe because of interaction between a=8T29|1|R|C|30 B=8T29|1|R|G|46
  4 Basepair    30   46 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left 12 Right 15
pMakeMotifModelFromSSF:   4  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:   5   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8T29|1|R|G|18
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8T29|1|R|G|19
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8T29|1|R|G|20
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8T29|1|R|A|21
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8T29|1|R|C|22
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8T29|1|R|C|23
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8T29|1|R|U|24
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8T29|1|R|A|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8T29|1|R|C|26
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8T29|1|R|C|27
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8T29|1|R|A|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8T29|1|R|G|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-11 8.1893e-10 8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 … ]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGGACCUACCC'
           RightLetter: 'AAC'
               Comment: ' // Basepair G17 - C50 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8T29|1|R|G|18'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8T29|1|R|G|19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 14
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8T29|1|R|G|20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8T29|1|R|A|21'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8T29|1|R|C|22'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8T29|1|R|C|23'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8T29|1|R|U|24'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8T29|1|R|A|25'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8T29|1|R|C|26'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 11
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             LeftIndex: 11
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8T29|1|R|C|27'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 12
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             LeftIndex: 12
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8T29|1|R|A|48'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 12
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 26
             LeftIndex: 12
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8T29|1|R|G|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             LeftIndex: 12
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 28
             LeftIndex: 12
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A29 - G47 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 29
             LeftIndex: 13
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C30 - G46 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 29

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 31
             LeftIndex: 14
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 14
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 17
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 17
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 17
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 17
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 17
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 17
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 17
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 17
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 17
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 17
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 17
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 17
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 17
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 17
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 17
pMakeMotifModelFromSSF:  18   Initial Left 10 Right 17
pMakeMotifModelFromSSF:  19     Fixed Left 10 Right 17
pMakeMotifModelFromSSF:  20   Initial Left 11 Right 17
pMakeMotifModelFromSSF:  21     Fixed Left 11 Right 17
pMakeMotifModelFromSSF:  22   Initial Left 12 Right 17
pMakeMotifModelFromSSF:  23     Fixed Left 12 Right 17
pMakeMotifModelFromSSF:  24   Initial Left 12 Right 16
pMakeMotifModelFromSSF:  25     Fixed Left 12 Right 16
pMakeMotifModelFromSSF:  26   Initial Left 12 Right 15
pMakeMotifModelFromSSF:  27  Basepair Left 12 Right 15
pMakeMotifModelFromSSF:  28  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  29   Hairpin Left 14 Right 13
pNextNodeJunction: Found a hairpin at node 29
pNextNodeJunction: Found a hairpin at node 29

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_19516.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.3269

Timestamp 18-Jul-2025 22:47:04
pMakeSCFGModels: Making JAR3D model for motif group IL_19668.1, number 81 of 411
pMakeNodes starting loop:     a=3E5C|1|A|A|27 B=3E5C|1|A|U|14
  2 Basepair    27   14 AU cWW 
No need to probe because of interaction between a=3E5C|1|A|G|28 B=3E5C|1|A|A|13
  3 Basepair    28   13 GA cWW 
pMakeNodes probe for inserts:  a=3E5C|1|A|A|29 B=3E5C|1|A|G|12
    Insertion on left  3E5C|1|A|A|29
    Insertion on left  3E5C|1|A|G|31
pMakeNodesProbeForInsertions:  a 3E5C|1|A|C|32 interacts with 3E5C|1|A|G|12
pMakeNodesProbeForInsertions:  B 3E5C|1|A|G|12 interacts with 3E5C|1|A|C|32
pMakeNodesProbeForInsertions:  B 3E5C|1|A|G|12 interacts with 3E5C|1|A|C|32
pMakeNodes probed for insert:  a=3E5C|1|A|C|32 B=3E5C|1|A|G|12
  4 Basepair    32   12 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3E5C|1|A|U|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3E5C|1|A|A|27
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A27 - U14 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAG'
           RightLetter: 'A'
               Comment: ' // Basepair G28 - A13 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3E5C|1|A|U|14'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3E5C|1|A|A|27'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C32 - G12 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_19668.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.6625
   -7.6632

Timestamp 18-Jul-2025 22:47:04
pMakeSCFGModels: Making JAR3D model for motif group IL_19852.1, number 82 of 411
pMakeNodes starting loop:     a=8EYU|1|A|A|16 B=8EYU|1|A|U|38
  2 Basepair    16   38 AU cWW 
pMakeNodes probe for inserts:  a=8EYU|1|A|G|17 B=8EYU|1|A|A|37
pMakeNodesProbeForInsertions:  a 8EYU|1|A|G|17 interacts with 8EYU|1|A|U|26
pMakeNodesProbeForInsertions:  B 8EYU|1|A|A|37 interacts with 8EYU|1|A|U|26
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8EYU|1|A|A|37 interacts with 8EYU|1|A|U|26
pMakeNodes probed for insert:  a=8EYU|1|A|G|17 B=8EYU|1|A|A|37
pMakeNodes making a cluster near strand break a=8EYU|1|A|G|17 B=8EYU|1|A|A|37
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 9 and then 10 to 10
aa is 9 bb is 10
  3 Cluster   8EYU|1|A|G|17:8EYU|1|A|U|26 8EYU|1|A|A|37:8EYU|1|A|A|37
    LR Inter  8EYU|1|A|U|26 8EYU|1|A|A|37 cWW 
    LL Inter  8EYU|1|A|G|18 8EYU|1|A|G|22 cWH 
    LL Inter  8EYU|1|A|G|20 8EYU|1|A|G|24 cWH 
    LL Inter  8EYU|1|A|G|21 8EYU|1|A|G|25 cWH 
    LL Inter  8EYU|1|A|G|17 8EYU|1|A|U|26 tWH 
pMakeNodesCluster a=10 B=9 at the end
pMakeNodesCluster a=10 B=9 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8  9 Right 10
pMakeMotifModelFromSSF:   4   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A16 - U38 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5 6 7 8 9]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGGGGGGU'
           RightLetter: 'A'
               Comment: ' // Cluster node 8EYU|1|A|G|17:8EYU|1|A|U|26 and 8EYU|1|A|A|37:8EYU|1|A|A|37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2578

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8  9 Right 10
pMakeMotifModelFromSSF:   4   Initial Left 10 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_19852.1 allow insertions from initial node 4?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_19852.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.2429

Timestamp 18-Jul-2025 22:47:05
pMakeSCFGModels: Making JAR3D model for motif group IL_19897.3, number 83 of 411
pMakeNodes starting loop:     a=7EOG|1|A|C|28 B=7EOG|1|A|G|15
  2 Basepair    28   15 CG cWW 
pMakeNodes probe for inserts:  a=7EOG|1|A|C|29 B=7EOG|1|A|U|14
    Insertion on left  7EOG|1|A|C|29
    Insertion on left  7EOG|1|A|A|30
    Insertion on left  7EOG|1|A|A|31
pMakeNodesProbeForInsertions:  a 7EOG|1|A|U|32 interacts with 7EOG|1|A|U|35
pMakeNodesProbeForInsertions:  B 7EOG|1|A|U|14 interacts with 7EOG|1|A|A|36
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 7EOG|1|A|U|14 interacts with 7EOG|1|A|A|36
pMakeNodes probed for insert:  a=7EOG|1|A|U|32 B=7EOG|1|A|U|14
pMakeNodes making a cluster near strand break a=7EOG|1|A|U|32 B=7EOG|1|A|U|14
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 9 and then 10 to 10
aa is 9 bb is 10
  3 Cluster   7EOG|1|A|U|32:7EOG|1|A|A|36 7EOG|1|A|U|14:7EOG|1|A|U|14
    LR Inter  7EOG|1|A|A|36 7EOG|1|A|U|14 cWW 
    LL Inter  7EOG|1|A|U|32 7EOG|1|A|U|35 tWH 
    Left  strand conserved insertion 7EOG|1|A|C|33 at position 2
    Left  strand conserved insertion 7EOG|1|A|G|34 at position 3
pMakeNodesCluster a=10 B=9 at the end
pMakeNodesCluster a=10 B=9 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  5  6  7  8  9 Right 10
pMakeMotifModelFromSSF:   4   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7EOG|1|A|G|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7EOG|1|A|C|28
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7EOG|1|A|C|29
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CCAA'
           RightLetter: 'G'
               Comment: ' // Basepair C28 - G15 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7EOG|1|A|G|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 1

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7EOG|1|A|C|28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7EOG|1|A|C|29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 10
             LeftIndex: [5 6 7 8 9]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UCGUA'
           RightLetter: 'U'
               Comment: ' // Cluster node 7EOG|1|A|U|32:7EOG|1|A|A|36 and 7EOG|1|A|U|14:7EOG|1|A|U|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 1

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9   Cluster Left  5  6  7  8  9 Right 10
pMakeMotifModelFromSSF:  10   Initial Left 10 Right  9
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 11
pUpdateModelWithSSF: IL_19897.3 allow insertions from initial node 10?
ans =

    0.9739    0.0249    0.0012


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9739    0.0249    0.0012


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_19897.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0474
   -6.0474

Timestamp 18-Jul-2025 22:47:05
pMakeSCFGModels: Making JAR3D model for motif group IL_20031.1, number 84 of 411
pMakeNodes starting loop:     a=8D29|1|F|C|21 B=8D29|1|F|G|11
  2 Basepair    21   11 CG cWW 
pMakeNodes probe for inserts:  a=8D29|1|F|C|22 B=8D29|1|F|A|10
    Insertion on left  8D29|1|F|C|22
    Insertion on left  8D29|1|F|C|23
pMakeNodesProbeForInsertions:  a 8D29|1|F|U|25 interacts with 8D29|1|F|A|10
pMakeNodesProbeForInsertions:  B 8D29|1|F|A|10 interacts with 8D29|1|F|U|25
pMakeNodesProbeForInsertions:  B 8D29|1|F|A|10 interacts with 8D29|1|F|U|25
pMakeNodes probed for insert:  a=8D29|1|F|U|25 B=8D29|1|F|A|10
  3 Basepair    25   10 UA cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8D29|1|F|G|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8D29|1|F|C|21
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CCC'
           RightLetter: 'G'
               Comment: ' // Basepair C21 - G11 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8D29|1|F|G|11'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8D29|1|F|C|21'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U25 - A10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_20031.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.6710
   -6.6705

Timestamp 18-Jul-2025 22:47:05
pMakeSCFGModels: Making JAR3D model for motif group IL_20047.1, number 85 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|U|2173 B=8P9A|1|AR|G|2161
  2 Basepair  2173 2161 UG cWW 
No need to probe because of interaction between a=8P9A|1|AR|G|2174 B=8P9A|1|AR|G|2160
  3 Basepair  2174 2160 GG tWW 
No need to probe because of interaction between a=8P9A|1|AR|U|2176 B=8P9A|1|AR|A|2158
  4 Basepair  2176 2158 UA tWW 
No need to probe because of interaction between a=8P9A|1|AR|G|2177 B=8P9A|1|AR|G|2157
  5 Basepair  2177 2157 GG tSS 
pMakeNodes probe for inserts:  a=8P9A|1|AR|A|2178 B=8P9A|1|AR|C|2156
    Insertion on left  8P9A|1|AR|A|2178
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|G|2180 interacts with 8P9A|1|AR|C|2156
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|C|2156 interacts with 8P9A|1|AR|G|2180
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|C|2156 interacts with 8P9A|1|AR|G|2180
pMakeNodes probed for insert:  a=8P9A|1|AR|G|2180 B=8P9A|1|AR|C|2156
  6 Basepair  2180 2156 GC cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|G|2160
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U2173 - G2161 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G2174 - G2160 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U2176 - A2158 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'G'
               Comment: ' // Basepair G2177 - G2157 tSS '
              NumLoops: []
                  Edge: 12
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|G|2160'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2180 - C2156 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_20047.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.5682
   -6.5687

Timestamp 18-Jul-2025 22:47:06
pMakeSCFGModels: Making JAR3D model for motif group IL_20245.1, number 86 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|G|2107 B=5J7L|1|DA|U|2182
  2 Basepair  2107 2182 GU cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|2108 B=5J7L|1|DA|U|2181
    Insertion on left  5J7L|1|DA|A|2108
    Insertion on left  5J7L|1|DA|U|2109
    Insertion on left  5J7L|1|DA|G|2110
    Insertion on left  5J7L|1|DA|G|2112
    Insertion on left  5J7L|1|DA|U|2113
    Insertion on left  5J7L|1|DA|G|2120
    Insertion on right 5J7L|1|DA|U|2181
    Insertion on right 5J7L|1|DA|U|2180
    Insertion on right 5J7L|1|DA|C|2179
    Insertion on right 5J7L|1|DA|C|2178
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|G|2121 interacts with 5J7L|1|DA|C|2177
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|2177 interacts with 5J7L|1|DA|G|2121
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|2177 interacts with 5J7L|1|DA|G|2121
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5J7L|1|DA|G|2121 B=5J7L|1|DA|C|2177
pMakeNodes making a cluster near strand break a=5J7L|1|DA|G|2121 B=5J7L|1|DA|C|2177
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 8 to 8 and then 12 to 13
aa is 8 bb is 12
  3 Cluster   5J7L|1|DA|G|2121:5J7L|1|DA|G|2121 5J7L|1|DA|A|2176:5J7L|1|DA|C|2177
    LR Inter  5J7L|1|DA|G|2121 5J7L|1|DA|A|2176 wat 
    LR Inter  5J7L|1|DA|G|2121 5J7L|1|DA|C|2177 cWW 
pMakeNodesCluster a=9 B=11 at the end
pMakeNodesCluster a=9 B=11 at the end
pMakeNodes probe for inserts:  a=5J7L|1|DA|U|2122 B=5J7L|1|DA|C|2175
    Insertion on left  5J7L|1|DA|U|2122
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|G|2123 interacts with 5J7L|1|DA|C|2175
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|2175 interacts with 5J7L|1|DA|G|2123
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|2175 interacts with 5J7L|1|DA|G|2123
  4 Initial   2122 (1 insertion) and 2175 (0 insertion)
pMakeNodes probed for insert:  a=5J7L|1|DA|G|2123 B=5J7L|1|DA|C|2175
  5 Basepair  2123 2175 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3   Cluster Left  8 Right 12 13
pMakeMotifModelFromSSF:   4   Initial Left  9 Right 11
pMakeMotifModelFromSSF:   5  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   6   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|2108
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|U|2109
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2110
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|U|2111
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2112
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|U|2113
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|G|2123
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|U|2122
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|G|2121
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|G|2120
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2115
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
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                  Edge: [18×18 double]
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                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
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Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
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       rightLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAUGGUG'
           RightLetter: 'CCUUU'
               Comment: ' // Basepair G2107 - U2182 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|2108'
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                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
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                  PIns: [1.0000e-05 1.0000]
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Node 4

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 17
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
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Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: []
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        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
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           MiddleIndex: 11
                     P: []
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Node 7

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 8

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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           RightLetter: []
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                     Z: []
           MiddleIndex: []
                     P: []
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Node 9

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 10

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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           RightLetter: []
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                     Z: []
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                     P: []
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Node 11

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 12

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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                     Z: []
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Node 13

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 14

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 15

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 16

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Node 17

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 18

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 20

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 21

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Node 22

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 24
             LeftIndex: 8
            RightIndex: [12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: 'AC'
               Comment: ' // Cluster node 5J7L|1|DA|G|2121:5J7L|1|DA|G|2121 and 5J7L|1|DA|A|2176:5J7L|1|DA|C|2177'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2]
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2532

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|U|2122 - 5J7L|1|DA|C|2175 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 26
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|2115'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 28
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2123 - C2175 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 30
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 17
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 17
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 17
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 17
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 17
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 17
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 17
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 17
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 17
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 17
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 17
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 17
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 17
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 16
pMakeMotifModelFromSSF:  17     Fixed Left  8 Right 16
pMakeMotifModelFromSSF:  18   Initial Left  8 Right 15
pMakeMotifModelFromSSF:  19     Fixed Left  8 Right 15
pMakeMotifModelFromSSF:  20   Initial Left  8 Right 14
pMakeMotifModelFromSSF:  21     Fixed Left  8 Right 14
pMakeMotifModelFromSSF:  22   Initial Left  8 Right 13
pMakeMotifModelFromSSF:  23   Cluster Left  8 Right 12 13
pMakeMotifModelFromSSF:  24   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  25     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  26   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  27  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  28   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 28
pNextNodeJunction: Found a hairpin at node 28

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_20245.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -18.0765

Timestamp 18-Jul-2025 22:47:06
pMakeSCFGModels: Making JAR3D model for motif group IL_20463.1, number 87 of 411
pMakeNodes starting loop:     a=5DDP|1|A|U|50 B=5DDP|1|A|A|29
  2 Basepair    50   29 UA cWW 
No need to probe because of interaction between a=5DDP|1|A|G|51 B=5DDP|1|A|A|28
  3 Basepair    51   28 GA tSH 
No need to probe because of interaction between a=5DDP|1|A|A|52 B=5DDP|1|A|U|27
pMakeNodes making a cluster near strand break a=5DDP|1|A|A|52 B=5DDP|1|A|U|27
pMakeNodesCluster: amax is 11 bmin is 12, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 3 and then 15 to 16
aa is 3 bb is 15
  4 Cluster   5DDP|1|A|A|52:5DDP|1|A|A|52 5DDP|1|A|G|26:5DDP|1|A|U|27
    LR Inter  5DDP|1|A|A|52 5DDP|1|A|U|27 tHW 
    RR Inter  5DDP|1|A|G|26 5DDP|1|A|U|27 cSH 
pMakeNodesCluster a=4 B=14 at the end
pMakeNodesCluster a=4 B=14 at the end
No need to probe because of interaction between a=5DDP|1|A|A|53 B=5DDP|1|A|A|25
  5 Basepair    53   25 AA tHH 
pMakeNodes probe for inserts:  a=5DDP|1|A|G|54 B=5DDP|1|A|A|24
    Insertion on right 5DDP|1|A|A|24
pMakeNodesProbeForInsertions:  a 5DDP|1|A|G|54 interacts with 5DDP|1|A|A|56
pMakeNodesProbeForInsertions:  B 5DDP|1|A|G|23 interacts with 5DDP|1|A|C|60
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 5DDP|1|A|G|23 interacts with 5DDP|1|A|C|60
pMakeNodes probed for insert:  a=5DDP|1|A|G|54 B=5DDP|1|A|G|23
pMakeNodes making a cluster near strand break a=5DDP|1|A|G|54 B=5DDP|1|A|G|23
pMakeNodesCluster: amax is 11 bmin is 12, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 11 and then 12 to 12
aa is 11 bb is 12
  6 Cluster   5DDP|1|A|G|54:5DDP|1|A|C|60 5DDP|1|A|G|23:5DDP|1|A|G|23
    LR Inter  5DDP|1|A|C|60 5DDP|1|A|G|23 cWW 
    LL Inter  5DDP|1|A|G|54 5DDP|1|A|A|56 cWH 
    Left  strand conserved insertion 5DDP|1|A|C|55 at position 2
    Left  strand conserved insertion 5DDP|1|A|A|57 at position 4
    Left  strand conserved insertion 5DDP|1|A|C|58 at position 5
    Left  strand conserved insertion 5DDP|1|A|G|59 at position 6
pMakeNodesCluster a=12 B=11 at the end
pMakeNodesCluster a=12 B=11 at the end
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4   Cluster Left  3 Right 15 16
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 14
pMakeMotifModelFromSSF:   6   Cluster Left  5  6  7  8  9 10 11 Right 12
pMakeMotifModelFromSSF:   7   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5DDP|1|A|C|55
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U50 - A29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G51 - A28 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: 3
            RightIndex: [15 16]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: 'GU'
               Comment: ' // Cluster node 5DDP|1|A|A|52:5DDP|1|A|A|52 and 5DDP|1|A|G|26:5DDP|1|A|U|27'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2]
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'AA'
               Comment: ' // Basepair A53 - A25 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5DDP|1|A|C|55'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 4 5 6]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 10
             LeftIndex: [5 6 7 8 9 10 11]
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCAACGC'
           RightLetter: 'G'
               Comment: ' // Cluster node 5DDP|1|A|G|54:5DDP|1|A|C|60 and 5DDP|1|A|G|23:5DDP|1|A|G|23'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 4 5 6]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 12
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 12
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4   Cluster Left  3 Right 15 16
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 14
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right 14
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right 13
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9   Cluster Left  5  6  7  8  9 10 11 Right 12
pMakeMotifModelFromSSF:  10   Initial Left 12 Right 11
pMakeMotifModelFromSSF:  11   Hairpin Left 12 Right 11
pNextNodeJunction: Found a hairpin at node 11
pUpdateModelWithSSF: IL_20463.1 allow insertions from initial node 10?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_20463.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.8739

Timestamp 18-Jul-2025 22:47:07
pMakeSCFGModels: Making JAR3D model for motif group IL_21001.1, number 88 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|C|3084 B=8P9A|1|AR|G|3059
  2 Basepair  3084 3059 CG cWW 
pMakeNodes probe for inserts:  a=8P9A|1|AR|G|3085 B=8P9A|1|AR|U|3057
    Insertion on left  8P9A|1|AR|G|3085
    Insertion on left  8P9A|1|AR|A|3086
    Insertion on left  8P9A|1|AR|A|3087
    Insertion on right 8P9A|1|AR|U|3057
    Insertion on right 8P9A|1|AR|U|3055
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|G|3088 interacts with 8P9A|1|AR|U|3054
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|U|3054 interacts with 8P9A|1|AR|G|3088
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|U|3054 interacts with 8P9A|1|AR|G|3088
pMakeNodes probed for insert:  a=8P9A|1|AR|G|3088 B=8P9A|1|AR|U|3054
  3 Basepair  3088 3054 GU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|U|3055
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|U|3056
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|U|3057
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|G|3085
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|C|3084
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGAA'
           RightLetter: 'UUG'
               Comment: ' // Basepair C3084 - G3059 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|U|3055'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|U|3056'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|U|3057'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|G|3085'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|C|3084'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G3088 - U3054 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  7
pMakeMotifModelFromSSF:  11     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  12   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  13  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  14   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_21001.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7383
   -5.7383
   -7.7282

Timestamp 18-Jul-2025 22:47:07
pMakeSCFGModels: Making JAR3D model for motif group IL_21173.1, number 89 of 411
pMakeNodes starting loop:     a=7UQ6|1|B|G|30 B=7UQ6|1|B|C|50
  2 Basepair    30   50 GC cWW 
pMakeNodes probe for inserts:  a=7UQ6|1|B|U|31 B=7UQ6|1|B|G|49
    Insertion on left  7UQ6|1|B|U|31
    Insertion on left  7UQ6|1|B|G|32
    Insertion on left  7UQ6|1|B|G|33
    Insertion on left  7UQ6|1|B|A|34
    Insertion on left  7UQ6|1|B|A|35
    Insertion on left  7UQ6|1|B|C|36
    Insertion on left  7UQ6|1|B|C|37
pMakeNodesProbeForInsertions:  a 7UQ6|1|B|C|38 interacts with 7UQ6|1|B|G|49
pMakeNodesProbeForInsertions:  B 7UQ6|1|B|G|49 interacts with 7UQ6|1|B|C|38
pMakeNodesProbeForInsertions:  B 7UQ6|1|B|G|49 interacts with 7UQ6|1|B|C|38
pMakeNodes probed for insert:  a=7UQ6|1|B|C|38 B=7UQ6|1|B|G|49
  3 Basepair    38   49 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   4   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7UQ6|1|B|U|31
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7UQ6|1|B|G|32
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7UQ6|1|B|G|33
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7UQ6|1|B|A|34
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7UQ6|1|B|A|35
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7UQ6|1|B|C|36
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7UQ6|1|B|C|37
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUGGAACC'
           RightLetter: 'C'
               Comment: ' // Basepair G30 - C50 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
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                  rpar: [17×1 double]
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Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
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        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7UQ6|1|B|U|31'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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    InteractionComment: {' // Hairpin for truncation'}
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Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7UQ6|1|B|G|32'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
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       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7UQ6|1|B|G|33'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
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                    id: []
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        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
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        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7UQ6|1|B|A|34'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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                     P: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7UQ6|1|B|A|35'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7UQ6|1|B|C|36'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7UQ6|1|B|C|37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C38 - G49 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  17  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  18   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a hairpin at node 18

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_21173.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.3948
   -5.3948

Timestamp 18-Jul-2025 22:47:07
pMakeSCFGModels: Making JAR3D model for motif group IL_21200.1, number 90 of 411
pMakeNodes starting loop:     a=6DLR|1|A|C|45 B=6DLR|1|A|G|15
  2 Basepair    45   15 CG cWW 
No need to probe because of interaction between a=6DLR|1|A|A|46 B=6DLR|1|A|A|14
  3 Basepair    46   14 AA tSH 
No need to probe because of interaction between a=6DLR|1|A|A|47 B=6DLR|1|A|U|13
  4 Basepair    47   13 AU tHW 
pMakeNodes probe for inserts:  a=6DLR|1|A|G|48 B=6DLR|1|A|C|12
    Insertion on left  6DLR|1|A|G|48
    Insertion on left  6DLR|1|A|U|49
pMakeNodesProbeForInsertions:  a 6DLR|1|A|G|50 interacts with 6DLR|1|A|C|12
pMakeNodesProbeForInsertions:  B 6DLR|1|A|C|12 interacts with 6DLR|1|A|G|50
pMakeNodesProbeForInsertions:  B 6DLR|1|A|C|12 interacts with 6DLR|1|A|G|50
pMakeNodes probed for insert:  a=6DLR|1|A|G|50 B=6DLR|1|A|C|12
  5 Basepair    50   12 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6DLR|1|A|G|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6DLR|1|A|C|45
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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                  rpar: []
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Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C45 - G15 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A46 - A14 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AGU'
           RightLetter: 'U'
               Comment: ' // Basepair A47 - U13 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6DLR|1|A|G|15'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6DLR|1|A|C|45'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G50 - C12 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  10   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_21200.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.1674
   -6.6767
   -6.3201
   -6.6566
   -6.3402
   -6.3402

Timestamp 18-Jul-2025 22:47:08
pMakeSCFGModels: Making JAR3D model for motif group IL_21630.1, number 91 of 411
pMakeNodes starting loop:     a=8Z8U|1|A|G|6 B=8Z8U|1|A|C|36
  2 Basepair     6   36 GC cWW 
pMakeNodes probe for inserts:  a=8Z8U|1|A|A|7 B=8Z8U|1|A|A|35
    Insertion on left  8Z8U|1|A|A|7
    Insertion on left  8Z8U|1|A|G|8
    Insertion on left  8Z8U|1|A|C|9
    Insertion on left  8Z8U|1|A|C|10
    Insertion on right 8Z8U|1|A|A|35
    Insertion on right 8Z8U|1|A|G|34
    Insertion on right 8Z8U|1|A|A|33
    Insertion on right 8Z8U|1|A|U|32
    Insertion on right 8Z8U|1|A|C|31
pMakeNodesProbeForInsertions:  a 8Z8U|1|A|C|11 interacts with 8Z8U|1|A|G|29
pMakeNodesProbeForInsertions:  B 8Z8U|1|A|G|30 interacts with 8Z8U|1|A|A|13
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8Z8U|1|A|G|30 interacts with 8Z8U|1|A|A|13
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8Z8U|1|A|C|11 B=8Z8U|1|A|G|30
pMakeNodes making a cluster near strand break a=8Z8U|1|A|C|11 B=8Z8U|1|A|G|30
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 6 to 9 and then 10 to 11
aa is 9 bb is 10
  3 Cluster   8Z8U|1|A|C|11:8Z8U|1|A|C|14 8Z8U|1|A|G|29:8Z8U|1|A|G|30
    LR Inter  8Z8U|1|A|C|11 8Z8U|1|A|G|29 tWH 
    LR Inter  8Z8U|1|A|C|14 8Z8U|1|A|G|29 cWW 
    LR Inter  8Z8U|1|A|A|13 8Z8U|1|A|G|30 cWW 
    LL Inter  8Z8U|1|A|C|11 8Z8U|1|A|A|13 cSH 
    Left  strand conserved insertion 8Z8U|1|A|A|12 at position 2
pMakeNodesCluster a=10 B=9 at the end
pMakeNodesCluster a=10 B=9 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3   Cluster Left  6  7  8  9 Right 10 11
pMakeMotifModelFromSSF:   4   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8Z8U|1|A|A|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8Z8U|1|A|G|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8Z8U|1|A|C|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8Z8U|1|A|C|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8Z8U|1|A|A|35
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8Z8U|1|A|G|34
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8Z8U|1|A|A|33
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8Z8U|1|A|U|32
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8Z8U|1|A|C|31
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [17×17 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAGCC'
           RightLetter: 'CUAGAC'
               Comment: ' // Basepair G6 - C36 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8Z8U|1|A|A|7'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: [1 2]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.0152

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8Z8U|1|A|G|8'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8Z8U|1|A|C|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8Z8U|1|A|C|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8Z8U|1|A|A|35'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8Z8U|1|A|G|34'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8Z8U|1|A|A|33'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8Z8U|1|A|U|32'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8Z8U|1|A|C|31'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 22
             LeftIndex: [6 7 8 9]
            RightIndex: [10 11]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CAAC'
           RightLetter: 'GG'
               Comment: ' // Cluster node 8Z8U|1|A|C|11:8Z8U|1|A|C|14 and 8Z8U|1|A|G|29:8Z8U|1|A|G|30'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: [1 2]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.0152

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 25
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 16
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 16
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 16
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 16
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 16
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 16
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 16
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 16
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 16
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 15
pMakeMotifModelFromSSF:  13     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:  14   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  15     Fixed Left  6 Right 14
pMakeMotifModelFromSSF:  16   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  17     Fixed Left  6 Right 13
pMakeMotifModelFromSSF:  18   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  19     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  20   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  21   Cluster Left  6  7  8  9 Right 10 11
pMakeMotifModelFromSSF:  22   Initial Left 10 Right  9
pMakeMotifModelFromSSF:  23   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 23
pUpdateModelWithSSF: IL_21630.1 allow insertions from initial node 22?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 23

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_21630.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.6160

Timestamp 18-Jul-2025 22:47:08
pMakeSCFGModels: Making JAR3D model for motif group IL_21667.1, number 92 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|U|64 B=8P9A|1|sR|A|86
  2 Basepair    64   86 UA cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|A|65 B=8P9A|1|sR|A|85
    Insertion on left  8P9A|1|sR|A|65
    Insertion on left  8P9A|1|sR|U|66
    Insertion on right 8P9A|1|sR|A|85
    Insertion on right 8P9A|1|sR|A|84
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|A|67 interacts with 8P9A|1|sR|G|83
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|G|83 interacts with 8P9A|1|sR|A|67
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|G|83 interacts with 8P9A|1|sR|A|67
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|sR|A|67 B=8P9A|1|sR|G|83
  3 Basepair    67   83 AG tHS 
pMakeNodes probe for inserts:  a=8P9A|1|sR|A|68 B=8P9A|1|sR|U|82
    Insertion on left  8P9A|1|sR|A|68
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|G|69 interacts with 8P9A|1|sR|U|82
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|82 interacts with 8P9A|1|sR|G|69
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|82 interacts with 8P9A|1|sR|G|69
pMakeNodes probed for insert:  a=8P9A|1|sR|G|69 B=8P9A|1|sR|U|82
  4 Basepair    69   82 GU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|A|65
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|U|66
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|A|85
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|A|84
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|A|68
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UAU'
           RightLetter: 'AAA'
               Comment: ' // Basepair U64 - A86 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|A|65'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|U|66'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|A|85'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|A|84'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'G'
               Comment: ' // Basepair A67 - G83 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|A|68'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G69 - U82 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 18
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   9     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  4 Right  8
pMakeMotifModelFromSSF:  11  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:  12     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  13   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  14  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  15   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a hairpin at node 15

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_21667.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8759
   -6.8759

Timestamp 18-Jul-2025 22:47:09
pMakeSCFGModels: Making JAR3D model for motif group IL_22373.1, number 93 of 411
pMakeNodes starting loop:     a=5U3G|1|B|G|10 B=5U3G|1|B|C|29
  2 Basepair    10   29 GC cWW 
No need to probe because of interaction between a=5U3G|1|B|G|11 B=5U3G|1|B|U|28
pMakeNodes making a cluster near strand break a=5U3G|1|B|G|11 B=5U3G|1|B|U|28
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 5 and then 6 to 7
aa is 5 bb is 6
  3 Cluster   5U3G|1|B|G|11:5U3G|1|B|C|14 5U3G|1|B|G|27:5U3G|1|B|U|28
    LR Inter  5U3G|1|B|C|14 5U3G|1|B|G|27 cWW 
    LR Inter  5U3G|1|B|G|11 5U3G|1|B|U|28 bif 
    LR Inter  5U3G|1|B|U|13 5U3G|1|B|U|28 cWW 
    LL Inter  5U3G|1|B|U|12 5U3G|1|B|U|13 cSH 
    LL Inter  5U3G|1|B|U|12 5U3G|1|B|C|14 cSH 
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5 Right  6  7
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G10 - C29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5]
            RightIndex: [6 7]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUUC'
           RightLetter: 'GU'
               Comment: ' // Cluster node 5U3G|1|B|G|11:5U3G|1|B|C|14 and 5U3G|1|B|G|27:5U3G|1|B|U|28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: [1 2]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0066

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5 Right  6  7
pMakeMotifModelFromSSF:   4   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_22373.1 allow insertions from initial node 4?
ans =

    0.9960    0.0040    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9960    0.0040    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_22373.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.5769
   -3.5769
   -3.5769
   -3.5769

Timestamp 18-Jul-2025 22:47:09
pMakeSCFGModels: Making JAR3D model for motif group IL_22551.4, number 94 of 411
pMakeNodes starting loop:     a=8CRE|1|1|G|2285 B=8CRE|1|1|C|2255
  2 Basepair  2285 2255 GC cWW 
pMakeNodes probe for inserts:  a=8CRE|1|1|C|2286 B=8CRE|1|1|G|2254
    Insertion on left  8CRE|1|1|C|2286
    Insertion on left  8CRE|1|1|A|2287
pMakeNodesProbeForInsertions:  a 8CRE|1|1|U|2288 interacts with 8CRE|1|1|G|2254
pMakeNodesProbeForInsertions:  B 8CRE|1|1|G|2254 interacts with 8CRE|1|1|U|2288
pMakeNodesProbeForInsertions:  B 8CRE|1|1|G|2254 interacts with 8CRE|1|1|U|2288
pMakeNodes probed for insert:  a=8CRE|1|1|U|2288 B=8CRE|1|1|G|2254
  3 Basepair  2288 2254 UG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|C|2255
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|G|2285
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GCA'
           RightLetter: 'C'
               Comment: ' // Basepair G2285 - C2255 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|C|2255'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|G|2285'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U2288 - G2254 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_22551.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.1441
   -4.1441
   -4.1441
   -3.9495
   -3.9495
   -3.9495
   -3.9495
   -6.8589
   -9.8788

Timestamp 18-Jul-2025 22:47:09
pMakeSCFGModels: Making JAR3D model for motif group IL_22564.1, number 95 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|G|1474 B=8CRE|1|CM|C|1505
pMakeNodes making a cluster near strand break a=8CRE|1|CM|G|1474 B=8CRE|1|CM|C|1505
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 6 to 9
aa is 5 bb is 6
  2 Cluster   8CRE|1|CM|G|1474:8CRE|1|CM|C|1481 8CRE|1|CM|G|1500:8CRE|1|CM|C|1505
    LR Inter  8CRE|1|CM|G|1474 8CRE|1|CM|G|1500 tSS 
    LR Inter  8CRE|1|CM|C|1481 8CRE|1|CM|G|1500 cWW 
    LR Inter  8CRE|1|CM|G|1474 8CRE|1|CM|C|1505 cWW 
    LL Inter  8CRE|1|CM|G|1480 8CRE|1|CM|C|1481 cSH 
    RR Inter  8CRE|1|CM|G|1500 8CRE|1|CM|A|1502 cSS 
    Left  strand conserved insertion 8CRE|1|CM|U|1475 at position 2
    Left  strand conserved insertion 8CRE|1|CM|A|1478 at position 3
    Right strand conserved insertion 8CRE|1|CM|A|1501 at position 2
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  3 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  6  7  8  9
pMakeMotifModelFromSSF:   3   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: [6 7 8 9]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUAGC'
           RightLetter: 'GAAC'
               Comment: ' // Cluster node 8CRE|1|CM|G|1474:8CRE|1|CM|C|1481 and 8CRE|1|CM|G|1500:8CRE|1|CM|C|1505'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
          LeftNotInter: [2 3]
         RightNotInter: 2
              NormCons: 0.0038

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  6  7  8  9
pMakeMotifModelFromSSF:   3   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 4
pUpdateModelWithSSF: IL_22564.1 allow insertions from initial node 3?
ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_22564.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.0598
   -9.5033

Timestamp 18-Jul-2025 22:47:10
pMakeSCFGModels: Making JAR3D model for motif group IL_22829.2, number 96 of 411
pMakeNodes starting loop:     a=8CRE|1|1|A|1879 B=8CRE|1|1|U|2327
  2 Basepair  1879 2327 AU cWW 
pMakeNodes probe for inserts:  a=8CRE|1|1|A|1880 B=8CRE|1|1|A|2326
    Insertion on left  8CRE|1|1|A|1880
pMakeNodesProbeForInsertions:  a 8CRE|1|1|U|1881 interacts with 8CRE|1|1|A|2326
pMakeNodesProbeForInsertions:  B 8CRE|1|1|A|2326 interacts with 8CRE|1|1|U|1881
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8CRE|1|1|A|2326 interacts with 8CRE|1|1|A|1883
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8CRE|1|1|U|1881 B=8CRE|1|1|A|2326
pMakeNodes making a cluster near strand break a=8CRE|1|1|U|1881 B=8CRE|1|1|A|2326
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 5 and then 10 to 10
aa is 5 bb is 10
  3 Cluster   8CRE|1|1|U|1881:8CRE|1|1|A|1883 8CRE|1|1|A|2326:8CRE|1|1|A|2326
    LR Inter  8CRE|1|1|U|1881 8CRE|1|1|A|2326 tSH 
    LR Inter  8CRE|1|1|A|1883 8CRE|1|1|A|2326 tHS 
    Left  strand conserved insertion 8CRE|1|1|A|1882 at position 2
pMakeNodesCluster a=6 B=9 at the end
pMakeNodesCluster a=6 B=9 at the end
No need to probe because of interaction between a=8CRE|1|1|U|1884 B=8CRE|1|1|U|2325
  4 Basepair  1884 2325 UU cWW 
No need to probe because of interaction between a=8CRE|1|1|G|1885 B=8CRE|1|1|C|2324
  5 Basepair  1885 2324 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  3  4  5 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|A|1880
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'U'
               Comment: ' // Basepair A1879 - U2327 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|A|1880'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2410

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [3 4 5]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAA'
           RightLetter: 'A'
               Comment: ' // Cluster node 8CRE|1|1|U|1881:8CRE|1|1|A|1883 and 8CRE|1|1|A|2326:8CRE|1|1|A|2326'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2410

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U1884 - U2325 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1885 - C2324 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5   Cluster Left  3  4  5 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_22829.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8665
   -6.8665
  -12.6477

Timestamp 18-Jul-2025 22:47:10
pMakeSCFGModels: Making JAR3D model for motif group IL_22854.4, number 97 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|G|1666 B=5J7L|1|DA|C|1994
  2 Basepair  1666 1994 GC cWW 
No need to probe because of interaction between a=5J7L|1|DA|G|1667 B=5J7L|1|DA|U|1993
pMakeNodes making a cluster near strand break a=5J7L|1|DA|G|1667 B=5J7L|1|DA|U|1993
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 11 to 13
aa is 4 bb is 11
  3 Cluster   5J7L|1|DA|G|1667:5J7L|1|DA|A|1669 5J7L|1|DA|U|1991:5J7L|1|DA|U|1993
    LR Inter  5J7L|1|DA|A|1668 5J7L|1|DA|U|1991 tHW 
    LR Inter  5J7L|1|DA|G|1667 5J7L|1|DA|U|1993 tSH 
    LR Inter  5J7L|1|DA|A|1669 5J7L|1|DA|U|1993 cWW 
    Right strand conserved insertion 5J7L|1|DA|G|1992 at position 2
pMakeNodesCluster a=5 B=10 at the end
pMakeNodesCluster a=5 B=10 at the end
pMakeNodes probe for inserts:  a=5J7L|1|DA|C|1670 B=5J7L|1|DA|C|1990
    Insertion on left  5J7L|1|DA|C|1670
    Insertion on left  5J7L|1|DA|U|1671
    Insertion on left  5J7L|1|DA|A|1672
    Insertion on left  5J7L|1|DA|G|1673
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|G|1674 interacts with 5J7L|1|DA|C|1990
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|1990 interacts with 5J7L|1|DA|G|1674
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|1990 interacts with 5J7L|1|DA|G|1674
  4 Initial   1670 (4 insertion) and 1990 (0 insertion)
pMakeNodes probed for insert:  a=5J7L|1|DA|G|1674 B=5J7L|1|DA|C|1990
  5 Basepair  1674 1990 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 11 12 13
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   6   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|1670
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|U|1671
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|1672
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|1673
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1666 - C1994 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4]
            RightIndex: [11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAA'
           RightLetter: 'UGU'
               Comment: ' // Cluster node 5J7L|1|DA|G|1667:5J7L|1|DA|A|1669 and 5J7L|1|DA|U|1991:5J7L|1|DA|U|1993'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: 2
              NormCons: 0.2514

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CUAG'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|C|1670 - 5J7L|1|DA|C|1990 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|1670'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|U|1671'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|1672'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|1673'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1674 - C1990 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 11 12 13
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_22854.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.5624
   -5.2631
   -6.0516
   -6.5981
   -7.3509
   -5.9389
   -5.9389

Timestamp 18-Jul-2025 22:47:11
pMakeSCFGModels: Making JAR3D model for motif group IL_23038.1, number 98 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|U|1737 B=8P9A|1|AR|A|1707
  2 Basepair  1737 1707 UA cWW 
No need to probe because of interaction between a=8P9A|1|AR|C|1738 B=8P9A|1|AR|C|1706
  3 Basepair  1738 1706 CC bif 
No need to probe because of interaction between a=8P9A|1|AR|U|1739 B=8P9A|1|AR|U|1705
  4 Basepair  1739 1705 UU tWH 
pMakeNodes probe for inserts:  a=8P9A|1|AR|U|1740 B=8P9A|1|AR|A|1704
    Insertion on right 8P9A|1|AR|A|1704
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|U|1740 interacts with 8P9A|1|AR|A|1741
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|U|1703 interacts with 8P9A|1|AR|U|1742
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|U|1703 interacts with 8P9A|1|AR|U|1742
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|AR|U|1740 B=8P9A|1|AR|U|1703
pMakeNodes making a cluster near strand break a=8P9A|1|AR|U|1740 B=8P9A|1|AR|U|1703
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 6 and then 9 to 9
aa is 6 bb is 9
  5 Cluster   8P9A|1|AR|U|1740:8P9A|1|AR|U|1742 8P9A|1|AR|U|1703:8P9A|1|AR|U|1703
    LR Inter  8P9A|1|AR|U|1742 8P9A|1|AR|U|1703 cWW 
    LL Inter  8P9A|1|AR|U|1740 8P9A|1|AR|A|1741 cSH 
pMakeNodesCluster a=7 B=8 at the end
pMakeNodesCluster a=7 B=8 at the end
No need to probe because of interaction between a=8P9A|1|AR|G|1743 B=8P9A|1|AR|U|1702
  6 Basepair  1743 1702 GU cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5   Cluster Left  4  5  6 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|U|1740
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1737 - A1707 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C1738 - C1706 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'AU'
               Comment: ' // Basepair U1739 - U1705 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|U|1740'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [4 5 6]
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAU'
           RightLetter: 'U'
               Comment: ' // Cluster node 8P9A|1|AR|U|1740:8P9A|1|AR|U|1742 and 8P9A|1|AR|U|1703:8P9A|1|AR|U|1703'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1743 - U1702 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7   Cluster Left  4  5  6 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  10   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_23038.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.0164
   -5.0164

Timestamp 18-Jul-2025 22:47:12
pMakeSCFGModels: Making JAR3D model for motif group IL_23774.1, number 99 of 411
pMakeNodes starting loop:     a=4V9F|1|0|G|2754 B=4V9F|1|0|C|2728
  2 Basepair  2754 2728 GC cWW 
No need to probe because of interaction between a=4V9F|1|0|G|2755 B=4V9F|1|0|A|2727
  3 Basepair  2755 2727 GA tSH 
pMakeNodes probe for inserts:  a=4V9F|1|0|U|2756 B=4V9F|1|0|G|2725
    Insertion on left  4V9F|1|0|U|2756
pMakeNodesProbeForInsertions:  a 4V9F|1|0|A|2757 interacts with 4V9F|1|0|G|2725
pMakeNodesProbeForInsertions:  B 4V9F|1|0|G|2725 interacts with 4V9F|1|0|A|2757
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4V9F|1|0|G|2725 interacts with 4V9F|1|0|A|2757
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4V9F|1|0|A|2757 B=4V9F|1|0|G|2725
  4 Basepair  2757 2725 AG tHS 
No need to probe because of interaction between a=4V9F|1|0|G|2758 B=4V9F|1|0|U|2724
  5 Basepair  2758 2724 GU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|U|2726
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2754 - C2728 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Basepair G2755 - A2727 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|U|2726'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A2757 - G2725 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G2758 - U2724 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_23774.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8605
   -8.1532
   -9.3324
   -8.5671
   -9.1439
   -9.1439
  -10.4087
   -8.3296
  -10.3944
   -7.8605
  -10.3795

Timestamp 18-Jul-2025 22:47:12
pMakeSCFGModels: Making JAR3D model for motif group IL_24134.1, number 100 of 411
pMakeNodes starting loop:     a=2VPL|1|B|C|33 B=2VPL|1|B|G|13
pMakeNodes making a cluster near strand break a=2VPL|1|B|C|33 B=2VPL|1|B|G|13
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 7 and then 10 to 12
aa is 7 bb is 10
  2 Cluster   2VPL|1|B|C|33:2VPL|1|B|A|39 2VPL|1|B|G|11:2VPL|1|B|G|13
    LR Inter  2VPL|1|B|A|39 2VPL|1|B|G|11 tHS 
    LR Inter  2VPL|1|B|C|33 2VPL|1|B|G|13 cWW 
    LR Inter  2VPL|1|B|A|39 2VPL|1|B|G|13 tSS 
    LL Inter  2VPL|1|B|C|33 2VPL|1|B|A|39 cSS 
    Left  strand conserved insertion 2VPL|1|B|G|34 at position 2
    Left  strand conserved insertion 2VPL|1|B|A|35 at position 3
    Left  strand conserved insertion 2VPL|1|B|G|36 at position 4
    Left  strand conserved insertion 2VPL|1|B|A|37 at position 5
    Left  strand conserved insertion 2VPL|1|B|A|38 at position 6
    Right strand conserved insertion 2VPL|1|B|A|12 at position 2
pMakeNodesCluster a=8 B=9 at the end
pMakeNodesCluster a=8 B=9 at the end
No need to probe because of interaction between a=2VPL|1|B|C|40 B=2VPL|1|B|G|10
  3 Basepair    40   10 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6  7 Right 10 11 12
pMakeMotifModelFromSSF:   3  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   4   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 0 0 0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5 6 7]
            RightIndex: [10 11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CGAGAAA'
           RightLetter: 'GAG'
               Comment: ' // Cluster node 2VPL|1|B|C|33:2VPL|1|B|A|39 and 2VPL|1|B|G|11:2VPL|1|B|G|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×10 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [10×2 double]
    InteractionComment: {1×10 cell}
      JunctionDeletion: []
          InterIndices: [10×2 double]
          LeftNotInter: [2 3 4 5 6]
         RightNotInter: 2
              NormCons: 0.0078
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C40 - G10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6  7 Right 10 11 12
pMakeMotifModelFromSSF:   3   Initial Left  8 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_24134.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.2755
   -4.7863
   -4.2755

Timestamp 18-Jul-2025 22:47:13
pMakeSCFGModels: Making JAR3D model for motif group IL_24254.1, number 101 of 411
pMakeNodes starting loop:     a=1UN6|1|F|U|72 B=1UN6|1|F|A|103
  2 Basepair    72  103 UA cWW 
No need to probe because of interaction between a=1UN6|1|F|U|73 B=1UN6|1|F|U|102
  3 Basepair    73  102 UU cWW 
No need to probe because of interaction between a=1UN6|1|F|A|74 B=1UN6|1|F|A|101
  4 Basepair    74  101 AA tHH 
pMakeNodes probe for inserts:  a=1UN6|1|F|G|75 B=1UN6|1|F|A|100
pMakeNodesProbeForInsertions:  a 1UN6|1|F|G|75 interacts with 1UN6|1|F|U|76
pMakeNodesProbeForInsertions:  B 1UN6|1|F|A|100 interacts with 1UN6|1|F|U|76
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 1UN6|1|F|A|100 interacts with 1UN6|1|F|U|76
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=1UN6|1|F|G|75 B=1UN6|1|F|A|100
pMakeNodes making a cluster near strand break a=1UN6|1|F|G|75 B=1UN6|1|F|A|100
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 10 to 10
aa is 5 bb is 10
  5 Cluster   1UN6|1|F|G|75:1UN6|1|F|U|76 1UN6|1|F|A|100:1UN6|1|F|A|100
    LR Inter  1UN6|1|F|U|76 1UN6|1|F|A|100 tWH 
    LL Inter  1UN6|1|F|G|75 1UN6|1|F|U|76 cSH 
pMakeNodesCluster a=6 B=9 at the end
pMakeNodesCluster a=6 B=9 at the end
No need to probe because of interaction between a=1UN6|1|F|A|77 B=1UN6|1|F|G|99
  6 Basepair    77   99 AG tHS 
No need to probe because of interaction between a=1UN6|1|F|C|78 B=1UN6|1|F|G|98
  7 Basepair    78   98 CG cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U72 - A103 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U73 - U102 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A74 - A101 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [4 5]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 1UN6|1|F|G|75:1UN6|1|F|U|76 and 1UN6|1|F|A|100:1UN6|1|F|A|100'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A77 - G99 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C78 - G98 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_24254.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.5592

Timestamp 18-Jul-2025 22:47:13
pMakeSCFGModels: Making JAR3D model for motif group IL_24499.1, number 102 of 411
pMakeNodes starting loop:     a=7ELQ|1|A|A|6 B=7ELQ|1|A|U|41
pMakeNodes making a cluster near strand break a=7ELQ|1|A|A|6 B=7ELQ|1|A|U|41
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 4 and then 12 to 12
aa is 4 bb is 12
  2 Cluster   7ELQ|1|A|A|6:7ELQ|1|A|A|9 7ELQ|1|A|U|41:7ELQ|1|A|U|41
    LR Inter  7ELQ|1|A|A|6 7ELQ|1|A|U|41 cWW 
    LR Inter  7ELQ|1|A|A|9 7ELQ|1|A|U|41 cWS 
    Left  strand conserved insertion 7ELQ|1|A|G|7 at position 2
    Left  strand conserved insertion 7ELQ|1|A|A|8 at position 3
pMakeNodesCluster a=5 B=11 at the end
pMakeNodesCluster a=5 B=11 at the end
No need to probe because of interaction between a=7ELQ|1|A|G|10 B=7ELQ|1|A|U|40
  3 Basepair    10   40 GU cWS 
pMakeNodes probe for inserts:  a=7ELQ|1|A|C|11 B=7ELQ|1|A|A|39
    Insertion on left  7ELQ|1|A|C|11
    Insertion on right 7ELQ|1|A|A|39
pMakeNodesProbeForInsertions:  a 7ELQ|1|A|G|12 interacts with 7ELQ|1|A|U|13
pMakeNodesProbeForInsertions:  B 7ELQ|1|A|A|38 interacts with 7ELQ|1|A|U|13
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 7ELQ|1|A|A|38 interacts with 7ELQ|1|A|U|13
pMakeNodes probed for insert:  a=7ELQ|1|A|G|12 B=7ELQ|1|A|A|38
pMakeNodes making a cluster near strand break a=7ELQ|1|A|G|12 B=7ELQ|1|A|A|38
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 7 to 8 and then 9 to 9
aa is 8 bb is 9
  4 Cluster   7ELQ|1|A|G|12:7ELQ|1|A|U|13 7ELQ|1|A|A|38:7ELQ|1|A|A|38
    LR Inter  7ELQ|1|A|U|13 7ELQ|1|A|A|38 cWW 
    LL Inter  7ELQ|1|A|G|12 7ELQ|1|A|U|13 cSH 
pMakeNodesCluster a=9 B=8 at the end
pMakeNodesCluster a=9 B=8 at the end
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right 11
pMakeMotifModelFromSSF:   4   Cluster Left  7  8 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7ELQ|1|A|C|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7ELQ|1|A|A|39
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 0 0 0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4]
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGAA'
           RightLetter: 'U'
               Comment: ' // Cluster node 7ELQ|1|A|A|6:7ELQ|1|A|A|9 and 7ELQ|1|A|U|41:7ELQ|1|A|U|41'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.2481
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GC'
           RightLetter: 'AU'
               Comment: ' // Basepair G10 - U40 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7ELQ|1|A|C|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2555
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7ELQ|1|A|A|39'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 10
             LeftIndex: [7 8]
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 7ELQ|1|A|G|12:7ELQ|1|A|U|13 and 7ELQ|1|A|A|38:7ELQ|1|A|A|38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2555
                  lpar: []
                  rpar: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 12
pMakeMotifModelFromSSF:   3   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  7 Right  9
pMakeMotifModelFromSSF:   9   Cluster Left  7  8 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  9 Right  8
pMakeMotifModelFromSSF:  11   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 11
pUpdateModelWithSSF: IL_24499.1 allow insertions from initial node 10?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_24499.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.4797

Timestamp 18-Jul-2025 22:47:14
pMakeSCFGModels: Making JAR3D model for motif group IL_25186.4, number 103 of 411
pMakeNodes starting loop:     a=7Q80|1|B|G|14 B=7Q80|1|C|C|35
  2 Basepair    14   35 GC cWW 
pMakeNodes probe for inserts:  a=7Q80|1|B|A|15 B=7Q80|1|C|A|33
    Insertion on left  7Q80|1|B|A|15
    Insertion on left  7Q80|1|B|C|16
    Insertion on right 7Q80|1|C|A|33
    Insertion on right 7Q80|1|C|C|32
pMakeNodesProbeForInsertions:  a 7Q80|1|B|C|17 interacts with 7Q80|1|C|A|31
pMakeNodesProbeForInsertions:  B 7Q80|1|C|A|31 interacts with 7Q80|1|B|C|17
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 7Q80|1|C|A|31 interacts with 7Q80|1|B|C|17
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=7Q80|1|B|C|17 B=7Q80|1|C|A|31
  3 Basepair    17   31 CA cWW 
No need to probe because of interaction between a=7Q80|1|B|C|18 B=7Q80|1|C|G|30
  4 Basepair    18   30 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7Q80|1|B|A|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7Q80|1|B|C|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7Q80|1|C|A|33
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7Q80|1|C|C|32
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAC'
           RightLetter: 'CAC'
               Comment: ' // Basepair G14 - C35 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7Q80|1|B|A|15'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7Q80|1|B|C|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7Q80|1|C|A|33'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7Q80|1|C|C|32'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C17 - A31 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C18 - G30 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  4 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_25186.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7388
   -5.7388
   -5.7388
   -5.7388
   -5.7388
  -16.0033

Timestamp 18-Jul-2025 22:47:14
pMakeSCFGModels: Making JAR3D model for motif group IL_25412.1, number 104 of 411
pMakeNodes starting loop:     a=1NTA|1|A|C|7 B=1NTA|1|B|G|114
  2 Basepair     7  114 CG cWW 
pMakeNodes probe for inserts:  a=1NTA|1|A|A|8 B=1NTA|1|B|C|113
    Insertion on left  1NTA|1|A|A|8
    Insertion on left  1NTA|1|A|U|11
    Insertion on left  1NTA|1|A|G|12
pMakeNodesProbeForInsertions:  a 1NTA|1|A|G|13 interacts with 1NTA|1|B|C|113
pMakeNodesProbeForInsertions:  B 1NTA|1|B|C|113 interacts with 1NTA|1|A|G|13
pMakeNodesProbeForInsertions:  B 1NTA|1|B|C|113 interacts with 1NTA|1|A|G|13
pMakeNodes probed for insert:  a=1NTA|1|A|G|13 B=1NTA|1|B|C|113
  3 Basepair    13  113 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1NTA|1|A|A|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1NTA|1|A|U|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1NTA|1|A|U|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAUG'
           RightLetter: 'G'
               Comment: ' // Basepair C7 - G114 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1NTA|1|A|A|8'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1NTA|1|A|U|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1NTA|1|A|U|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G13 - C113 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  10   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_25412.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.2890

Timestamp 18-Jul-2025 22:47:15
pMakeSCFGModels: Making JAR3D model for motif group IL_25463.1, number 105 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|C|977 B=8P9A|1|AR|G|1104
  2 Basepair   977 1104 CG cWW 
pMakeNodes probe for inserts:  a=8P9A|1|AR|G|978 B=8P9A|1|AR|A|1102
    Insertion on left  8P9A|1|AR|G|978
    Insertion on left  8P9A|1|AR|U|979
    Insertion on left  8P9A|1|AR|A|980
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|U|981 interacts with 8P9A|1|AR|A|1102
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|A|1102 interacts with 8P9A|1|AR|U|981
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|A|1102 interacts with 8P9A|1|AR|U|981
pMakeNodes probed for insert:  a=8P9A|1|AR|U|981 B=8P9A|1|AR|A|1102
  3 Basepair   981 1102 UA cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|G|978
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|U|979
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|A|980
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGUA'
           RightLetter: 'G'
               Comment: ' // Basepair C977 - G1104 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|G|978'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|U|979'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|A|980'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U981 - A1102 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  10   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_25463.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.6856
   -7.6857

Timestamp 18-Jul-2025 22:47:15
pMakeSCFGModels: Making JAR3D model for motif group IL_25573.1, number 106 of 411
pMakeNodes starting loop:     a=1F1T|1|A|G|23 B=1F1T|1|A|C|10
pMakeNodes making a cluster near strand break a=1F1T|1|A|G|23 B=1F1T|1|A|C|10
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 8 to 8
aa is 5 bb is 8
  2 Cluster   1F1T|1|A|G|23:1F1T|1|A|A|27 1F1T|1|A|C|10:1F1T|1|A|C|10
    LR Inter  1F1T|1|A|G|23 1F1T|1|A|C|10 cWW 
    LL Inter  1F1T|1|A|G|23 1F1T|1|A|A|27 tSW 
    Left  strand conserved insertion 1F1T|1|A|G|24 at position 2
    Left  strand conserved insertion 1F1T|1|A|5BU|25 at position 3
    Left  strand conserved insertion 1F1T|1|A|A|26 at position 4
pMakeNodesCluster a=6 B=7 at the end
pMakeNodesCluster a=6 B=7 at the end
No need to probe because of interaction between a=1F1T|1|A|C|28 B=1F1T|1|A|G|8
  3 Basepair    28    8 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 0 0 0 0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGUAA'
           RightLetter: 'C'
               Comment: ' // Cluster node 1F1T|1|A|G|23:1F1T|1|A|A|27 and 1F1T|1|A|C|10:1F1T|1|A|C|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 0.2497
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C28 - G8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  8
pMakeMotifModelFromSSF:   3   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_25573.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.6057

Timestamp 18-Jul-2025 22:47:15
pMakeSCFGModels: Making JAR3D model for motif group IL_25872.4, number 107 of 411
pMakeNodes starting loop:     a=1CSL|1|A|G|46 B=1CSL|1|B|C|74
  2 Basepair    46   74 GC cWW 
No need to probe because of interaction between a=1CSL|1|A|G|47 B=1CSL|1|B|A|73
  3 Basepair    47   73 GA cWW 
No need to probe because of interaction between a=1CSL|1|A|G|48 B=1CSL|1|B|G|71
  4 Basepair    48   71 GG cWH 
No need to probe because of interaction between a=1CSL|1|A|C|49 B=1CSL|1|B|G|70
  5 Basepair    49   70 CG cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G46 - C74 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G47 - A73 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G48 - G71 cWH '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C49 - G70 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_25872.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0834
   -6.0834
   -7.4164
   -6.0035
   -8.7026

Timestamp 18-Jul-2025 22:47:16
pMakeSCFGModels: Making JAR3D model for motif group IL_26222.2, number 108 of 411
pMakeNodes starting loop:     a=4WF9|1|X|G|909 B=4WF9|1|X|C|957
pMakeNodes making a cluster near strand break a=4WF9|1|X|G|909 B=4WF9|1|X|C|957
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 6 to 9
aa is 5 bb is 6
  2 Cluster   4WF9|1|X|G|909:4WF9|1|X|U|913 4WF9|1|X|A|954:4WF9|1|X|C|957
    LR Inter  4WF9|1|X|C|910 4WF9|1|X|A|954 tWH 
    LR Inter  4WF9|1|X|U|913 4WF9|1|X|A|954 cWW 
    LR Inter  4WF9|1|X|G|909 4WF9|1|X|C|957 cWW 
    LR Inter  4WF9|1|X|C|912 4WF9|1|X|C|957 cWS 
    LL Inter  4WF9|1|X|G|909 4WF9|1|X|A|911 tSW 
    LL Inter  4WF9|1|X|C|910 4WF9|1|X|C|912 cSH 
    Right strand conserved insertion 4WF9|1|X|A|955 at position 2
    Right strand conserved insertion 4WF9|1|X|A|956 at position 3
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  3 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  6  7  8  9
pMakeMotifModelFromSSF:   3   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: [6 7 8 9]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCACU'
           RightLetter: 'AAAC'
               Comment: ' // Cluster node 4WF9|1|X|G|909:4WF9|1|X|U|913 and 4WF9|1|X|A|954:4WF9|1|X|C|957'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [2 3]
              NormCons: 0.0012

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  6  7  8  9
pMakeMotifModelFromSSF:   3   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 4
pUpdateModelWithSSF: IL_26222.2 allow insertions from initial node 3?
ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_26222.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.1973
   -2.1973
   -2.1973
   -2.1973
   -3.8625
   -3.8625

Timestamp 18-Jul-2025 22:47:17
pMakeSCFGModels: Making JAR3D model for motif group IL_26307.2, number 109 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|239 B=5J7L|1|DA|G|258
  2 Basepair   239  258 CG cWW 
No need to probe because of interaction between a=5J7L|1|DA|C|240 B=5J7L|1|DA|C|257
  3 Basepair   240  257 CC tSH 
No need to probe because of interaction between a=5J7L|1|DA|A|241 B=5J7L|1|DA|A|256
  4 Basepair   241  256 AA tHH 
pMakeNodes probe for inserts:  a=5J7L|1|DA|G|242 B=5J7L|1|DA|A|255
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|G|242 interacts with 5J7L|1|DA|U|243
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|255 interacts with 5J7L|1|DA|U|243
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|255 interacts with 5J7L|1|DA|U|243
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5J7L|1|DA|G|242 B=5J7L|1|DA|A|255
pMakeNodes making a cluster near strand break a=5J7L|1|DA|G|242 B=5J7L|1|DA|A|255
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 10 to 10
aa is 5 bb is 10
  5 Cluster   5J7L|1|DA|G|242:5J7L|1|DA|U|243 5J7L|1|DA|A|255:5J7L|1|DA|A|255
    LR Inter  5J7L|1|DA|U|243 5J7L|1|DA|A|255 tWH 
    LL Inter  5J7L|1|DA|G|242 5J7L|1|DA|U|243 cSH 
pMakeNodesCluster a=6 B=9 at the end
pMakeNodesCluster a=6 B=9 at the end
No need to probe because of interaction between a=5J7L|1|DA|A|244 B=5J7L|1|DA|G|254
  6 Basepair   244  254 AG tHS 
No need to probe because of interaction between a=5J7L|1|DA|G|245 B=5J7L|1|DA|C|253
  7 Basepair   245  253 GC cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C239 - G258 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C240 - C257 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A241 - A256 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [4 5]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 5J7L|1|DA|G|242:5J7L|1|DA|U|243 and 5J7L|1|DA|A|255:5J7L|1|DA|A|255'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A244 - G254 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G245 - C253 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_26307.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8707
   -8.0133
   -8.1464
   -7.6895
   -7.6895
   -8.7545
   -8.5715
   -7.7063
   -9.2047

Timestamp 18-Jul-2025 22:47:18
pMakeSCFGModels: Making JAR3D model for motif group IL_26598.1, number 110 of 411
pMakeNodes starting loop:     a=7JRS|1|B|G|104 B=7JRS|1|B|C|29
  2 Basepair   104   29 GC cWW 
pMakeNodes probe for inserts:  a=7JRS|1|B|G|105 B=7JRS|1|B|G|28
    Insertion on left  7JRS|1|B|G|105
    Insertion on left  7JRS|1|B|C|106
    Insertion on left  7JRS|1|B|G|107
    Insertion on left  7JRS|1|B|U|108
    Insertion on left  7JRS|1|B|C|109
    Insertion on left  7JRS|1|B|C|110
pMakeNodesProbeForInsertions:  a 7JRS|1|B|C|111 interacts with 7JRS|1|B|G|28
pMakeNodesProbeForInsertions:  B 7JRS|1|B|G|28 interacts with 7JRS|1|B|C|111
pMakeNodesProbeForInsertions:  B 7JRS|1|B|G|28 interacts with 7JRS|1|B|C|111
pMakeNodes probed for insert:  a=7JRS|1|B|C|111 B=7JRS|1|B|G|28
  3 Basepair   111   28 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   4   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRS|1|B|C|29
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRS|1|B|G|104
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRS|1|B|G|105
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRS|1|B|C|106
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRS|1|B|G|107
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRS|1|B|U|108
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGCGUCC'
           RightLetter: 'C'
               Comment: ' // Basepair G104 - C29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRS|1|B|C|29'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRS|1|B|G|104'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRS|1|B|G|105'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRS|1|B|C|106'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRS|1|B|G|107'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRS|1|B|U|108'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C111 - G28 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  9
pMakeMotifModelFromSSF:  12   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  14   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  15  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  16   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a hairpin at node 16

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_26598.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.4565
   -6.1646
   -5.4565
   -6.1646
   -8.1646

Timestamp 18-Jul-2025 22:47:18
pMakeSCFGModels: Making JAR3D model for motif group IL_26685.1, number 111 of 411
pMakeNodes starting loop:     a=3IGI|1|A|U|234 B=3IGI|1|A|G|129
  2 Basepair   234  129 UG cWW 
pMakeNodes probe for inserts:  a=3IGI|1|A|U|235 B=3IGI|1|A|G|128
    Insertion on left  3IGI|1|A|U|235
    Insertion on left  3IGI|1|A|A|237
pMakeNodesProbeForInsertions:  a 3IGI|1|A|U|238 interacts with 3IGI|1|A|G|128
pMakeNodesProbeForInsertions:  B 3IGI|1|A|G|128 interacts with 3IGI|1|A|U|238
pMakeNodesProbeForInsertions:  B 3IGI|1|A|G|128 interacts with 3IGI|1|A|U|238
pMakeNodes probed for insert:  a=3IGI|1|A|U|238 B=3IGI|1|A|G|128
  3 Basepair   238  128 UG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|G|129
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|U|234
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UUA'
           RightLetter: 'G'
               Comment: ' // Basepair U234 - G129 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IGI|1|A|G|129'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IGI|1|A|U|234'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U238 - G128 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_26685.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.7358

Timestamp 18-Jul-2025 22:47:19
pMakeSCFGModels: Making JAR3D model for motif group IL_26728.3, number 112 of 411
pMakeNodes starting loop:     a=7EOG|1|A|U|40 B=7EOG|1|A|G|10
  2 Basepair    40   10 UG cWW 
pMakeNodes probe for inserts:  a=7EOG|1|A|G|41 B=7EOG|1|A|G|9
    Insertion on right 7EOG|1|A|G|9
pMakeNodesProbeForInsertions:  a 7EOG|1|A|G|41 interacts with 7EOG|1|A|U|42
pMakeNodesProbeForInsertions:  B 7EOG|1|A|U|8 interacts with 7EOG|1|A|U|42
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 7EOG|1|A|U|8 interacts with 7EOG|1|A|U|42
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=7EOG|1|A|G|41 B=7EOG|1|A|U|8
pMakeNodes making a cluster near strand break a=7EOG|1|A|G|41 B=7EOG|1|A|U|8
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 7 to 7
aa is 4 bb is 7
  3 Cluster   7EOG|1|A|G|41:7EOG|1|A|C|43 7EOG|1|A|U|8:7EOG|1|A|U|8
    LR Inter  7EOG|1|A|U|42 7EOG|1|A|U|8 cWW 
    LL Inter  7EOG|1|A|G|41 7EOG|1|A|U|42 cSH 
    LL Inter  7EOG|1|A|U|42 7EOG|1|A|C|43 cSH 
pMakeNodesCluster a=5 B=6 at the end
pMakeNodesCluster a=5 B=6 at the end
No need to probe because of interaction between a=7EOG|1|A|G|44 B=7EOG|1|A|C|7
  4 Basepair    44    7 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7EOG|1|A|C|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'GG'
               Comment: ' // Basepair U40 - G10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7EOG|1|A|C|43'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0870

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [2 3 4]
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUC'
           RightLetter: 'U'
               Comment: ' // Cluster node 7EOG|1|A|G|41:7EOG|1|A|C|43 and 7EOG|1|A|U|8:7EOG|1|A|U|8'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0870

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G44 - C7 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  7
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_26728.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.1475
   -5.1475

Timestamp 18-Jul-2025 22:47:19
pMakeSCFGModels: Making JAR3D model for motif group IL_26793.1, number 113 of 411
pMakeNodes starting loop:     a=7ZO1|1|A|G|5 B=7ZO1|1|C|DC|15
  2 Basepair     5   15 GC cWW 
pMakeNodes probe for inserts:  a=7ZO1|1|A|A|6 B=7ZO1|1|C|DC|14
    Insertion on left  7ZO1|1|A|A|6
pMakeNodesProbeForInsertions:  a 7ZO1|1|A|G|7 interacts with 7ZO1|1|C|DC|14
pMakeNodesProbeForInsertions:  B 7ZO1|1|C|DC|14 interacts with 7ZO1|1|A|G|7
pMakeNodesProbeForInsertions:  B 7ZO1|1|C|DC|14 interacts with 7ZO1|1|A|G|7
pMakeNodes probed for insert:  a=7ZO1|1|A|G|7 B=7ZO1|1|C|DC|14
  3 Basepair     7   14 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7ZO1|1|A|A|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'C'
               Comment: ' // Basepair G5 - C15 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7ZO1|1|A|A|6'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G7 - C14 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_26793.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.4310
   -5.3361
   -3.4353
   -3.7945
   -4.2272
   -3.4310
   -3.4786
   -4.2272
   -4.2272
   -4.2272
   -3.4353
   -3.4786
   -3.4786
   -4.2724
   -3.4310
   -3.4353

Timestamp 18-Jul-2025 22:47:20
pMakeSCFGModels: Making JAR3D model for motif group IL_27393.10, number 114 of 411
pMakeNodes starting loop:     a=4PHY|1|A|C|5 B=4PHY|1|B|G|41
  2 Basepair     5   41 CG cWW 
pMakeNodes probe for inserts:  a=4PHY|1|A|U|6 B=4PHY|1|B|G|40
    Insertion on left  4PHY|1|A|U|6
    Insertion on left  4PHY|1|A|C|7
    Insertion on left  4PHY|1|A|C|8
    Insertion on left  4PHY|1|A|C|9
    Insertion on left  4PHY|1|A|C|10
    Insertion on left  4PHY|1|A|A|11
pMakeNodesProbeForInsertions:  a 4PHY|1|A|C|12 interacts with 4PHY|1|B|G|40
pMakeNodesProbeForInsertions:  B 4PHY|1|B|G|40 interacts with 4PHY|1|A|C|12
pMakeNodesProbeForInsertions:  B 4PHY|1|B|G|40 interacts with 4PHY|1|A|C|12
pMakeNodes probed for insert:  a=4PHY|1|A|C|12 B=4PHY|1|B|G|40
  3 Basepair    12   40 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   4   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4PHY|1|A|U|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4PHY|1|A|C|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4PHY|1|A|C|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4PHY|1|A|C|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4PHY|1|A|C|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4PHY|1|A|A|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CUCCCCA'
           RightLetter: 'G'
               Comment: ' // Basepair C5 - G41 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4PHY|1|A|U|6'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                  lpar: [17×1 double]
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Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
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                  lpar: []
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Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4PHY|1|A|C|7'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4PHY|1|A|C|8'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4PHY|1|A|C|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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      InsertionComment: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4PHY|1|A|C|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
    InteractionComment: []
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          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4PHY|1|A|A|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
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          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C12 - G40 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  9
pMakeMotifModelFromSSF:  12   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  14   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  15  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  16   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a hairpin at node 16

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_27393.10_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.9535
   -5.4427
   -5.4427

Timestamp 18-Jul-2025 22:47:20
pMakeSCFGModels: Making JAR3D model for motif group IL_28026.3, number 115 of 411
pMakeNodes starting loop:     a=4LFB|1|A|G|409 B=4LFB|1|A|C|433
  2 Basepair   409  433 GC cWW 
No need to probe because of interaction between a=4LFB|1|A|G|410 B=4LFB|1|A|A|432
  3 Basepair   410  432 GA tSH 
pMakeNodes probe for inserts:  a=4LFB|1|A|A|411 B=4LFB|1|A|A|431
pMakeNodesProbeForInsertions:  a 4LFB|1|A|A|411 interacts with 4LFB|1|A|A|430
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|431 interacts with 4LFB|1|A|U|429
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|431 interacts with 4LFB|1|A|U|429
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodes probed for insert:  a=4LFB|1|A|A|411 B=4LFB|1|A|A|431
pMakeNodes making a cluster near strand break a=4LFB|1|A|A|411 B=4LFB|1|A|A|431
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 7 and then 10 to 13
aa is 7 bb is 10
  4 Cluster   4LFB|1|A|A|411:4LFB|1|A|A|415 4LFB|1|A|G|428:4LFB|1|A|A|431
    LR Inter  4LFB|1|A|G|413 4LFB|1|A|G|428 tSS 
    LR Inter  4LFB|1|A|A|415 4LFB|1|A|G|428 tHH 
    LR Inter  4LFB|1|A|A|411 4LFB|1|A|A|430 tWH 
    LR Inter  4LFB|1|A|A|414 4LFB|1|A|A|430 tHW 
    RR Inter  4LFB|1|A|U|429 4LFB|1|A|A|431 cWH 
    Left  strand conserved insertion 4LFB|1|A|A|412 at position 2
pMakeNodesCluster a=8 B=9 at the end
pMakeNodesCluster a=8 B=9 at the end
No need to probe because of interaction between a=4LFB|1|A|G|416 B=4LFB|1|A|U|427
  5 Basepair   416  427 GU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6  7 Right 10 11 12 13
pMakeMotifModelFromSSF:   5  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   6   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G409 - C433 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G410 - A432 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4 5 6 7]
            RightIndex: [10 11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAGAA'
           RightLetter: 'GUAA'
               Comment: ' // Cluster node 4LFB|1|A|A|411:4LFB|1|A|A|415 and 4LFB|1|A|G|428:4LFB|1|A|A|431'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.1290

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G416 - U427 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6  7 Right 10 11 12 13
pMakeMotifModelFromSSF:   5   Initial Left  8 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   7   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_28026.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8838
   -6.5426

Timestamp 18-Jul-2025 22:47:21
pMakeSCFGModels: Making JAR3D model for motif group IL_28037.2, number 116 of 411
pMakeNodes starting loop:     a=3BNN|1|C|G|17 B=3BNN|1|D|C|5
  2 Basepair    17    5 GC cWW 
No need to probe because of interaction between a=3BNN|1|C|U|18 B=3BNN|1|D|U|4
  3 Basepair    18    4 UU cWW 
No need to probe because of interaction between a=3BNN|1|C|C|19 B=3BNN|1|D|G|3
  4 Basepair    19    3 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G17 - C5 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U18 - U4 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C19 - G3 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_28037.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.7996
   -2.7996
   -2.7996
   -2.9760
   -2.7996
   -2.7996
   -2.7996
   -2.9760
   -2.7996
   -2.7996
   -2.7996
   -2.9760
   -2.7996
   -2.9760
   -3.7252
   -3.3887
   -2.7996
   -3.6274
   -5.9573
   -2.7996
   -2.7996
   -3.3887
   -3.7727
   -2.7996
   -3.7727
   -2.7996
   -2.7996
   -2.7996
   -3.2123
   -3.3125
   -3.7602
   -3.2123
   -6.7541
   -3.7252
   -2.7996
   -3.7602
   -2.7996
   -2.7996
   -3.7252
   -2.7996
   -2.7996
   -7.0252
   -3.5839
   -3.2123
   -3.3887
   -3.3887
   -6.9627
   -3.7602
   -2.7996
   -2.7996
   -4.4117
   -4.9847
   -4.6482
   -2.7996
   -4.9847
   -3.3887
   -2.7996
   -3.3887
   -4.9847
   -3.7252
   -3.7252
   -4.6482
   -3.3887
   -2.9760
   -6.1304

Timestamp 18-Jul-2025 22:47:22
pMakeSCFGModels: Making JAR3D model for motif group IL_28304.1, number 117 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|A|1224 B=8P9A|1|sR|U|1259
  2 Basepair  1224 1259 AU cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|U|1225 B=8P9A|1|sR|U|1258
    Insertion on left  8P9A|1|sR|U|1225
    Insertion on left  8P9A|1|sR|A|1226
    Insertion on left  8P9A|1|sR|A|1227
    Insertion on left  8P9A|1|sR|G|1229
    Insertion on left  8P9A|1|sR|A|1230
    Insertion on right 8P9A|1|sR|U|1258
    Insertion on right 8P9A|1|sR|A|1256
    Insertion on right 8P9A|1|sR|G|1255
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|U|1231 interacts with 8P9A|1|sR|U|1254
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|1254 interacts with 8P9A|1|sR|U|1231
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|1254 interacts with 8P9A|1|sR|U|1231
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|sR|U|1231 B=8P9A|1|sR|U|1254
  3 Basepair  1231 1254 UU cWW 
No need to probe because of interaction between a=8P9A|1|sR|U|1232 B=8P9A|1|sR|U|1253
  4 Basepair  1232 1253 UU cWW 
No need to probe because of interaction between a=8P9A|1|sR|G|1233 B=8P9A|1|sR|C|1252
  5 Basepair  1233 1252 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:   5  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   6   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|U|1225
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|A|1226
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|A|1227
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|G|1228
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|G|1229
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|A|1256
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|G|1255
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|U|1254
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AUAAGA'
           RightLetter: 'GAUU'
               Comment: ' // Basepair A1224 - U1259 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|U|1225'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|A|1226'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|A|1227'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|G|1228'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|G|1229'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|A|1256'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|G|1255'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|U|1254'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U1231 - U1254 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 21
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U1232 - U1253 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1233 - C1252 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 15
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 15
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 15
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 15
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 15
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 15
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 15
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 15
pMakeMotifModelFromSSF:  14   Initial Left  7 Right 14
pMakeMotifModelFromSSF:  15     Fixed Left  7 Right 14
pMakeMotifModelFromSSF:  16   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  17     Fixed Left  7 Right 13
pMakeMotifModelFromSSF:  18   Initial Left  7 Right 12
pMakeMotifModelFromSSF:  19  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:  20  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  21  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  22   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Found a hairpin at node 22

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_28304.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.5071

Timestamp 18-Jul-2025 22:47:23
pMakeSCFGModels: Making JAR3D model for motif group IL_28564.1, number 118 of 411
pMakeNodes starting loop:     a=6DTD|1|C|U|28 B=6DTD|1|C|G|11
  2 Basepair    28   11 UG cWW 
No need to probe because of interaction between a=6DTD|1|C|A|29 B=6DTD|1|C|U|10
  3 Basepair    29   10 AU cWW 
pMakeNodes probe for inserts:  a=6DTD|1|C|A|30 B=6DTD|1|C|U|8
    Insertion on left  6DTD|1|C|A|30
pMakeNodesProbeForInsertions:  a 6DTD|1|C|A|31 interacts with 6DTD|1|C|U|8
pMakeNodesProbeForInsertions:  B 6DTD|1|C|U|8 interacts with 6DTD|1|C|A|31
pMakeNodesProbeForInsertions:  B 6DTD|1|C|U|8 interacts with 6DTD|1|C|A|31
pMakeNodes probed for insert:  a=6DTD|1|C|A|31 B=6DTD|1|C|U|8
  4 Basepair    31    8 AU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6DTD|1|C|U|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U28 - G11 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'U'
               Comment: ' // Basepair A29 - U10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6DTD|1|C|U|10'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A31 - U8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_28564.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.7743

Timestamp 18-Jul-2025 22:47:23
pMakeSCFGModels: Making JAR3D model for motif group IL_28788.1, number 119 of 411
pMakeNodes starting loop:     a=4ERD|1|C|G|146 B=4ERD|1|D|C|123
  2 Basepair   146  123 GC cWW 
pMakeNodes probe for inserts:  a=4ERD|1|C|G|147 B=4ERD|1|D|C|120
    Insertion on left  4ERD|1|C|G|147
    Insertion on right 4ERD|1|D|C|120
pMakeNodesProbeForInsertions:  a 4ERD|1|C|A|148 interacts with 4ERD|1|D|U|119
pMakeNodesProbeForInsertions:  B 4ERD|1|D|U|119 interacts with 4ERD|1|C|A|148
pMakeNodesProbeForInsertions:  B 4ERD|1|D|U|119 interacts with 4ERD|1|C|A|148
pMakeNodes probed for insert:  a=4ERD|1|C|A|148 B=4ERD|1|D|U|119
  3 Basepair   148  119 AU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4ERD|1|C|G|147
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4ERD|1|D|C|120
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: 'CC'
               Comment: ' // Basepair G146 - C123 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4ERD|1|C|G|147'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4ERD|1|D|C|120'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A148 - U119 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_28788.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.6470

Timestamp 18-Jul-2025 22:47:23
pMakeSCFGModels: Making JAR3D model for motif group IL_29198.2, number 120 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|G|991 B=8P9A|1|AR|U|1058
  2 Basepair   991 1058 GU cWW 
No need to probe because of interaction between a=8P9A|1|AR|A|992 B=8P9A|1|AR|A|1057
  3 Basepair   992 1057 AA cWW 
No need to probe because of interaction between a=8P9A|1|AR|G|993 B=8P9A|1|AR|U|1056
  4 Basepair   993 1056 GU bif 
pMakeNodes probe for inserts:  a=8P9A|1|AR|G|994 B=8P9A|1|AR|A|1055
    Insertion on right 8P9A|1|AR|A|1055
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|G|994 interacts with 8P9A|1|AR|U|995
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|A|1054 interacts with 8P9A|1|AR|U|995
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|A|1054 interacts with 8P9A|1|AR|U|995
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|AR|G|994 B=8P9A|1|AR|A|1054
pMakeNodes making a cluster near strand break a=8P9A|1|AR|G|994 B=8P9A|1|AR|A|1054
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 10 to 10
aa is 5 bb is 10
  5 Cluster   8P9A|1|AR|G|994:8P9A|1|AR|U|995 8P9A|1|AR|A|1054:8P9A|1|AR|A|1054
    LR Inter  8P9A|1|AR|U|995 8P9A|1|AR|A|1054 tWH 
    LL Inter  8P9A|1|AR|G|994 8P9A|1|AR|U|995 cSH 
pMakeNodesCluster a=6 B=9 at the end
pMakeNodesCluster a=6 B=9 at the end
No need to probe because of interaction between a=8P9A|1|AR|A|996 B=8P9A|1|AR|A|1053
  6 Basepair   996 1053 AA tHS 
No need to probe because of interaction between a=8P9A|1|AR|A|997 B=8P9A|1|AR|U|1052
  7 Basepair   997 1052 AU cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|A|1055
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G991 - U1058 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A992 - A1057 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'AU'
               Comment: ' // Basepair G993 - U1056 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|A|1055'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [4 5]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 8P9A|1|AR|G|994:8P9A|1|AR|U|995 and 8P9A|1|AR|A|1054:8P9A|1|AR|A|1054'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A996 - A1053 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A997 - U1052 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7   Cluster Left  4  5 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  10  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  11   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_29198.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.5051
   -7.5051
   -8.4915
   -8.5192

Timestamp 18-Jul-2025 22:47:24
pMakeSCFGModels: Making JAR3D model for motif group IL_29223.1, number 121 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|U|117 B=8P9A|1|sR|A|299
  2 Basepair   117  299 UA cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|U|118 B=8P9A|1|sR|C|298
    Insertion on left  8P9A|1|sR|U|118
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|A|119 interacts with 8P9A|1|sR|C|298
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|C|298 interacts with 8P9A|1|sR|A|119
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|C|298 interacts with 8P9A|1|sR|A|119
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|sR|A|119 B=8P9A|1|sR|C|298
  3 Basepair   119  298 AC tHS 
No need to probe because of interaction between a=8P9A|1|sR|U|120 B=8P9A|1|sR|U|297
  4 Basepair   120  297 UU cWW 
No need to probe because of interaction between a=8P9A|1|sR|U|121 B=8P9A|1|sR|U|296
  5 Basepair   121  296 UU cWW 
No need to probe because of interaction between a=8P9A|1|sR|U|122 B=8P9A|1|sR|A|295
  6 Basepair   122  295 UA cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|U|118
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UU'
           RightLetter: 'A'
               Comment: ' // Basepair U117 - A299 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|U|118'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A119 - C298 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U120 - U297 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U121 - U296 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U122 - A295 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_29223.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.2659
   -6.2659

Timestamp 18-Jul-2025 22:47:24
pMakeSCFGModels: Making JAR3D model for motif group IL_29346.2, number 122 of 411
pMakeNodes starting loop:     a=5J7L|1|AA|G|774 B=5J7L|1|AA|C|805
  2 Basepair   774  805 GC cWW 
pMakeNodes probe for inserts:  a=5J7L|1|AA|G|775 B=5J7L|1|AA|U|804
    Insertion on left  5J7L|1|AA|G|775
    Insertion on left  5J7L|1|AA|G|776
    Insertion on left  5J7L|1|AA|A|777
pMakeNodesProbeForInsertions:  a 5J7L|1|AA|G|778 interacts with 5J7L|1|AA|U|804
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|U|804 interacts with 5J7L|1|AA|G|778
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|U|804 interacts with 5J7L|1|AA|G|778
pMakeNodes probed for insert:  a=5J7L|1|AA|G|778 B=5J7L|1|AA|U|804
  3 Basepair   778  804 GU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|G|775
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|G|776
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|A|777
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGGA'
           RightLetter: 'C'
               Comment: ' // Basepair G774 - C805 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|G|775'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|G|776'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|A|777'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G778 - U804 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  10   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_29346.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.3837
   -4.3837
   -8.8592

Timestamp 18-Jul-2025 22:47:25
pMakeSCFGModels: Making JAR3D model for motif group IL_29357.1, number 123 of 411
pMakeNodes starting loop:     a=8DK7|1|C|C|21 B=8DK7|1|C|G|11
  2 Basepair    21   11 CG cWW 
No need to probe because of interaction between a=8DK7|1|C|C|22 B=8DK7|1|C|A|10
  3 Basepair    22   10 CA bif 
pMakeNodes probe for inserts:  a=8DK7|1|C|C|23 B=8DK7|1|C|C|9
    Insertion on left  8DK7|1|C|C|23
pMakeNodesProbeForInsertions:  a 8DK7|1|C|U|24 interacts with 8DK7|1|C|U|6
pMakeNodesProbeForInsertions:  B 8DK7|1|C|C|9 interacts with 8DK7|1|C|G|26
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8DK7|1|C|C|9 interacts with 8DK7|1|C|G|26
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8DK7|1|C|U|24 B=8DK7|1|C|C|9
pMakeNodes making a cluster near strand break a=8DK7|1|C|U|24 B=8DK7|1|C|C|9
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 8 and then 13 to 16
aa is 8 bb is 13
  4 Cluster   8DK7|1|C|U|24:8DK7|1|C|A|29 8DK7|1|C|U|6:8DK7|1|C|C|9
    LR Inter  8DK7|1|C|U|24 8DK7|1|C|U|6 tHW 
    LR Inter  8DK7|1|C|A|29 8DK7|1|C|U|6 tHS 
    LR Inter  8DK7|1|C|G|26 8DK7|1|C|A|7 cWW 
    LR Inter  8DK7|1|C|G|27 8DK7|1|C|C|8 cWW 
    LR Inter  8DK7|1|C|G|26 8DK7|1|C|C|9 cWW 
    LL Inter  8DK7|1|C|U|24 8DK7|1|C|A|29 cWH 
    RR Inter  8DK7|1|C|A|7 8DK7|1|C|C|8 cSH 
    Left  strand conserved insertion 8DK7|1|C|U|25 at position 2
pMakeNodesCluster a=9 B=12 at the end
pMakeNodesCluster a=9 B=12 at the end
No need to probe because of interaction between a=8DK7|1|C|G|30 B=8DK7|1|C|A|5
  5 Basepair    30    5 GA cWW 
No need to probe because of interaction between a=8DK7|1|C|C|31 B=8DK7|1|C|G|4
  6 Basepair    31    4 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4   Cluster Left  4  5  6  7  8 Right 13 14 15 16
pMakeMotifModelFromSSF:   5  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:   6  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   7   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8DK7|1|C|U|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C21 - G11 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CC'
           RightLetter: 'A'
               Comment: ' // Basepair C22 - A10 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8DK7|1|C|U|6'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 3.1386e-04

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 7
             LeftIndex: [4 5 6 7 8]
            RightIndex: [13 14 15 16]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUGGA'
           RightLetter: 'UACC'
               Comment: ' // Cluster node 8DK7|1|C|U|24:8DK7|1|C|A|29 and 8DK7|1|C|U|6:8DK7|1|C|C|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 3.1386e-04

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G30 - A5 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C31 - G4 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 16
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 16
pMakeMotifModelFromSSF:   6   Cluster Left  4  5  6  7  8 Right 13 14 15 16
pMakeMotifModelFromSSF:   7   Initial Left  9 Right 12
pMakeMotifModelFromSSF:   8  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  10   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_29357.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.9155

Timestamp 18-Jul-2025 22:47:25
pMakeSCFGModels: Making JAR3D model for motif group IL_29471.1, number 124 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|2806 B=5J7L|1|DA|G|2892
  2 Basepair  2806 2892 CG cWW 
No need to probe because of interaction between a=5J7L|1|DA|U|2807 B=5J7L|1|DA|U|2891
  3 Basepair  2807 2891 UU cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|G|2808 B=5J7L|1|DA|G|2890
    Insertion on left  5J7L|1|DA|G|2808
    Insertion on left  5J7L|1|DA|A|2809
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|A|2810 interacts with 5J7L|1|DA|G|2890
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|2890 interacts with 5J7L|1|DA|A|2810
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|2890 interacts with 5J7L|1|DA|A|2810
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5J7L|1|DA|A|2810 B=5J7L|1|DA|G|2890
  4 Basepair  2810 2890 AG tHS 
No need to probe because of interaction between a=5J7L|1|DA|G|2811 B=5J7L|1|DA|C|2889
  5 Basepair  2811 2889 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2808
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|2809
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2806 - G2892 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGA'
           RightLetter: 'U'
               Comment: ' // Basepair U2807 - U2891 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|2808'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|2809'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A2810 - G2890 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2811 - C2889 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  10   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_29471.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.2861

Timestamp 18-Jul-2025 22:47:26
pMakeSCFGModels: Making JAR3D model for motif group IL_29826.1, number 125 of 411
pMakeNodes starting loop:     a=4V9F|1|0|C|1228 B=4V9F|1|0|G|1134
  2 Basepair  1228 1134 CG cWW 
No need to probe because of interaction between a=4V9F|1|0|C|1229 B=4V9F|1|0|A|1133
  3 Basepair  1229 1133 CA tSH 
No need to probe because of interaction between a=4V9F|1|0|A|1230 B=4V9F|1|0|A|1132
  4 Basepair  1230 1132 AA tHH 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|1232 B=4V9F|1|0|G|1131
    Insertion on left  4V9F|1|0|A|1232
    Insertion on left  4V9F|1|0|A|1233
    Insertion on right 4V9F|1|0|G|1131
    Insertion on right 4V9F|1|0|U|1130
    Insertion on right 4V9F|1|0|C|1129
    Insertion on right 4V9F|1|0|U|1128
    Insertion on right 4V9F|1|0|C|1127
    Insertion on right 4V9F|1|0|C|1126
    Insertion on right 4V9F|1|0|U|1125
    Insertion on right 4V9F|1|0|A|1124
pMakeNodesProbeForInsertions:  a 4V9F|1|0|G|1235 interacts with 4V9F|1|0|A|1236
pMakeNodesProbeForInsertions:  B 4V9F|1|0|U|1122 interacts with 4V9F|1|0|A|1242
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4V9F|1|0|U|1122 interacts with 4V9F|1|0|A|1242
pMakeNodes probed for insert:  a=4V9F|1|0|G|1235 B=4V9F|1|0|U|1122
pMakeNodes making a cluster near strand break a=4V9F|1|0|G|1235 B=4V9F|1|0|U|1122
pMakeNodesCluster: amax is 13 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 6 to 13 and then 14 to 14
aa is 13 bb is 14
  5 Cluster   4V9F|1|0|G|1235:4V9F|1|0|A|1242 4V9F|1|0|U|1122:4V9F|1|0|U|1122
    LR Inter  4V9F|1|0|A|1242 4V9F|1|0|U|1122 cWW 
    LL Inter  4V9F|1|0|G|1235 4V9F|1|0|A|1236 cSH 
    LL Inter  4V9F|1|0|C|1238 4V9F|1|0|G|1241 tWH 
    Left  strand conserved insertion 4V9F|1|0|U|1237 at position 3
    Left  strand conserved insertion 4V9F|1|0|G|1239 at position 5
    Left  strand conserved insertion 4V9F|1|0|G|1240 at position 6
pMakeNodesCluster a=14 B=13 at the end
pMakeNodesCluster a=14 B=13 at the end
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 25
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 25
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 24
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 23
pMakeMotifModelFromSSF:   5   Cluster Left  6  7  8  9 10 11 12 13 Right 14
pMakeMotifModelFromSSF:   6   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|U|1125
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|C|1126
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|A|1236
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|G|1235
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|U|1234
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|A|1233
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|A|1232
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|A|1231
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|A|1230
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|C|1229
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 25
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [25×25 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 25
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1228 - G1134 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 24
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C1229 - A1133 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAA'
           RightLetter: 'AUCCUCUGA'
               Comment: ' // Basepair A1230 - A1132 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 22
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|U|1125'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [3 5 6]
         RightNotInter: [1×0 double]
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 22
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 22
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|C|1126'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 14
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 22
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 22
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V9F|1|0|A|1236'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V9F|1|0|G|1235'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V9F|1|0|U|1234'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V9F|1|0|A|1233'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 6
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 6
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V9F|1|0|A|1232'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 6
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 6
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V9F|1|0|A|1231'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V9F|1|0|A|1230'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V9F|1|0|C|1229'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 26
             LeftIndex: [6 7 8 9 10 11 12 13]
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAUCGGGA'
           RightLetter: 'U'
               Comment: ' // Cluster node 4V9F|1|0|G|1235:4V9F|1|0|A|1242 and 4V9F|1|0|U|1122:4V9F|1|0|U|1122'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [3 5 6]
         RightNotInter: [1×0 double]
              NormCons: 1

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             LeftIndex: 14
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 29
             LeftIndex: 14
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 14
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 25
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 25
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 24
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 23
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 22
pMakeMotifModelFromSSF:   6   Initial Left  5 Right 22
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right 22
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 22
pMakeMotifModelFromSSF:   9     Fixed Left  6 Right 22
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 21
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 21
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 20
pMakeMotifModelFromSSF:  13     Fixed Left  6 Right 20
pMakeMotifModelFromSSF:  14   Initial Left  6 Right 19
pMakeMotifModelFromSSF:  15     Fixed Left  6 Right 19
pMakeMotifModelFromSSF:  16   Initial Left  6 Right 18
pMakeMotifModelFromSSF:  17     Fixed Left  6 Right 18
pMakeMotifModelFromSSF:  18   Initial Left  6 Right 17
pMakeMotifModelFromSSF:  19     Fixed Left  6 Right 17
pMakeMotifModelFromSSF:  20   Initial Left  6 Right 16
pMakeMotifModelFromSSF:  21     Fixed Left  6 Right 16
pMakeMotifModelFromSSF:  22   Initial Left  6 Right 15
pMakeMotifModelFromSSF:  23     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:  24   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  25   Cluster Left  6  7  8  9 10 11 12 13 Right 14
pMakeMotifModelFromSSF:  26   Initial Left 14 Right 13
pMakeMotifModelFromSSF:  27   Hairpin Left 14 Right 13
pNextNodeJunction: Found a hairpin at node 27
pUpdateModelWithSSF: IL_29826.1 allow insertions from initial node 26?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 27

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_29826.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -18.0383

Timestamp 18-Jul-2025 22:47:26
pMakeSCFGModels: Making JAR3D model for motif group IL_30441.1, number 126 of 411
pMakeNodes starting loop:     a=8GXB|1|B|G|6 B=8GXB|1|B|C|40
pMakeNodes making a cluster near strand break a=8GXB|1|B|G|6 B=8GXB|1|B|C|40
pMakeNodesCluster: amax is 11 bmin is 12, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 14 to 14
aa is 2 bb is 14
  2 Cluster   8GXB|1|B|G|6:8GXB|1|B|U|7 8GXB|1|B|C|40:8GXB|1|B|C|40
    LR Inter  8GXB|1|B|G|6 8GXB|1|B|C|40 cWW 
    LL Inter  8GXB|1|B|G|6 8GXB|1|B|U|7 cSH 
pMakeNodesCluster a=3 B=13 at the end
pMakeNodesCluster a=3 B=13 at the end
pMakeNodes probe for inserts:  a=8GXB|1|B|U|8 B=8GXB|1|B|A|39
pMakeNodesProbeForInsertions:  a 8GXB|1|B|U|8 interacts with 8GXB|1|B|G|15
pMakeNodesProbeForInsertions:  B 8GXB|1|B|A|39 interacts with 8GXB|1|B|G|15
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but a makes a more important one
pMakeNodesProbeForInsertions:  B 8GXB|1|B|A|39 interacts with 8GXB|1|B|G|15
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  3 Initial      8 (0 insertion) and   39 (0 insertion)
pMakeNodes probed for insert:  a=8GXB|1|B|U|8 B=8GXB|1|B|A|39
pMakeNodes making a cluster near strand break a=8GXB|1|B|U|8 B=8GXB|1|B|A|39
pMakeNodesCluster: amax is 11 bmin is 12, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 9 and then 13 to 13
aa is 9 bb is 13
  4 Cluster   8GXB|1|B|U|8:8GXB|1|B|G|15 8GXB|1|B|A|39:8GXB|1|B|A|39
    LR Inter  8GXB|1|B|G|15 8GXB|1|B|A|39 tSW 
    LL Inter  8GXB|1|B|U|8 8GXB|1|B|G|15 tHW 
    Left  strand conserved insertion 8GXB|1|B|C|10 at position 2
    Left  strand conserved insertion 8GXB|1|B|G|11 at position 3
    Left  strand conserved insertion 8GXB|1|B|U|12 at position 4
    Left  strand conserved insertion 8GXB|1|B|C|13 at position 5
    Left  strand conserved insertion 8GXB|1|B|C|14 at position 6
pMakeNodesCluster a=10 B=12 at the end
pMakeNodesCluster a=10 B=12 at the end
pMakeNodes probe for inserts:  a=8GXB|1|B|A|16 B=8GXB|1|B|C|38
    Insertion on left  8GXB|1|B|A|16
pMakeNodesProbeForInsertions:  a 8GXB|1|B|G|19 interacts with 8GXB|1|B|C|38
pMakeNodesProbeForInsertions:  B 8GXB|1|B|C|38 interacts with 8GXB|1|B|G|19
pMakeNodesProbeForInsertions:  B 8GXB|1|B|C|38 interacts with 8GXB|1|B|G|19
  5 Initial     16 (1 insertion) and   38 (0 insertion)
pMakeNodes probed for insert:  a=8GXB|1|B|G|19 B=8GXB|1|B|C|38
  6 Basepair    19   38 GC cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 14
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6  7  8  9 Right 13
pMakeMotifModelFromSSF:   5   Initial Left 10 Right 12
pMakeMotifModelFromSSF:   6  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:   7   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8GXB|1|B|G|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'C'
               Comment: ' // Cluster node 8GXB|1|B|G|6:8GXB|1|B|U|7 and 8GXB|1|B|C|40:8GXB|1|B|C|40'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2501
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 8GXB|1|B|U|8 - 8GXB|1|B|A|39 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4 5 6 7 8 9]
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UCGUCCG'
           RightLetter: 'A'
               Comment: ' // Cluster node 8GXB|1|B|U|8:8GXB|1|B|G|15 and 8GXB|1|B|A|39:8GXB|1|B|A|39'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7]
                 Right: 1
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
          LeftNotInter: [2 3 4 5 6]
         RightNotInter: [1×0 double]
              NormCons: 0.2689
                  lpar: []
                  rpar: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 10
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 8GXB|1|B|A|16 - 8GXB|1|B|C|38 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 10
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8GXB|1|B|G|15'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G19 - C38 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 12
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 14
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6  7  8  9 Right 13
pMakeMotifModelFromSSF:   5   Initial Left 10 Right 12
pMakeMotifModelFromSSF:   6     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:   7   Initial Left 11 Right 12
pMakeMotifModelFromSSF:   8  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:   9   Hairpin Left 12 Right 11
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_30441.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.9663

Timestamp 18-Jul-2025 22:47:27
pMakeSCFGModels: Making JAR3D model for motif group IL_30730.1, number 127 of 411
pMakeNodes starting loop:     a=7WIE|1|V|U|17 B=7WIE|1|V|A|45
pMakeNodes making a cluster near strand break a=7WIE|1|V|U|17 B=7WIE|1|V|A|45
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 4 and then 9 to 9
aa is 4 bb is 9
  2 Cluster   7WIE|1|V|U|17:7WIE|1|V|A|21 7WIE|1|V|A|45:7WIE|1|V|A|45
    LR Inter  7WIE|1|V|U|17 7WIE|1|V|A|45 cWW 
    LR Inter  7WIE|1|V|U|18 7WIE|1|V|A|45 tHS 
    LR Inter  7WIE|1|V|A|21 7WIE|1|V|A|45 cWS 
    LL Inter  7WIE|1|V|U|17 7WIE|1|V|A|20 cSH 
    LL Inter  7WIE|1|V|U|18 7WIE|1|V|A|21 cWH 
pMakeNodesCluster a=5 B=8 at the end
pMakeNodesCluster a=5 B=8 at the end
pMakeNodes probe for inserts:  a=7WIE|1|V|C|22 B=7WIE|1|V|U|44
    Insertion on left  7WIE|1|V|C|22
    Insertion on right 7WIE|1|V|U|44
pMakeNodesProbeForInsertions:  a 7WIE|1|V|G|25 interacts with 7WIE|1|V|C|43
pMakeNodesProbeForInsertions:  B 7WIE|1|V|C|43 interacts with 7WIE|1|V|G|25
pMakeNodesProbeForInsertions:  B 7WIE|1|V|C|43 interacts with 7WIE|1|V|G|25
  3 Initial     22 (1 insertion) and   44 (1 insertion)
pMakeNodes probed for insert:  a=7WIE|1|V|G|25 B=7WIE|1|V|C|43
  4 Basepair    25   43 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right  9
pMakeMotifModelFromSSF:   3   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7WIE|1|V|A|21
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7WIE|1|V|C|24
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 0 0 0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4]
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUAA'
           RightLetter: 'A'
               Comment: ' // Cluster node 7WIE|1|V|U|17:7WIE|1|V|A|21 and 7WIE|1|V|A|45:7WIE|1|V|A|45'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0027
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'U'
               Comment: ' // Initial node 7WIE|1|V|C|22 - 7WIE|1|V|U|44 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7WIE|1|V|A|21'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7WIE|1|V|C|24'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G25 - C43 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right  9
pMakeMotifModelFromSSF:   3   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   4     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  6 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_30730.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.8665
   -5.8665

Timestamp 18-Jul-2025 22:47:27
pMakeSCFGModels: Making JAR3D model for motif group IL_31084.1, number 128 of 411
pMakeNodes starting loop:     a=1L9A|1|B|U|181 B=1L9A|1|B|A|216
  2 Basepair   181  216 UA cWW 
pMakeNodes probe for inserts:  a=1L9A|1|B|G|182 B=1L9A|1|B|A|215
    Insertion on left  1L9A|1|B|G|182
    Insertion on left  1L9A|1|B|A|183
    Insertion on left  1L9A|1|B|A|184
    Insertion on left  1L9A|1|B|C|185
    Insertion on left  1L9A|1|B|C|186
    Insertion on right 1L9A|1|B|A|215
    Insertion on right 1L9A|1|B|A|214
    Insertion on right 1L9A|1|B|A|213
pMakeNodesProbeForInsertions:  a 1L9A|1|B|G|187 interacts with 1L9A|1|B|C|212
pMakeNodesProbeForInsertions:  B 1L9A|1|B|C|212 interacts with 1L9A|1|B|G|187
pMakeNodesProbeForInsertions:  B 1L9A|1|B|C|212 interacts with 1L9A|1|B|G|187
pMakeNodes probed for insert:  a=1L9A|1|B|G|187 B=1L9A|1|B|C|212
  3 Basepair   187  212 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1L9A|1|B|G|182
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1L9A|1|B|A|183
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1L9A|1|B|A|184
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1L9A|1|B|C|185
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1L9A|1|B|C|186
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1L9A|1|B|A|215
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1L9A|1|B|A|214
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1L9A|1|B|A|213
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGAACC'
           RightLetter: 'AAAA'
               Comment: ' // Basepair U181 - A216 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1L9A|1|B|G|182'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1L9A|1|B|A|183'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1L9A|1|B|A|184'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1L9A|1|B|C|185'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1L9A|1|B|C|186'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1L9A|1|B|A|215'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1L9A|1|B|A|214'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1L9A|1|B|A|213'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G187 - C212 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 22
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:  14   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  15     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  16   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  17     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  18   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  19  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  20   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Found a hairpin at node 20

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_31084.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2173

Timestamp 18-Jul-2025 22:47:28
pMakeSCFGModels: Making JAR3D model for motif group IL_31462.6, number 129 of 411
pMakeNodes starting loop:     a=8VFS|1|A|A|11 B=8VFS|1|B|U|18
  2 Basepair    11   18 AU cWW 
pMakeNodes probe for inserts:  a=8VFS|1|A|A|12 B=8VFS|1|B|C|17
    Insertion on left  8VFS|1|A|A|12
pMakeNodesProbeForInsertions:  a 8VFS|1|A|G|13 interacts with 8VFS|1|B|C|17
pMakeNodesProbeForInsertions:  B 8VFS|1|B|C|17 interacts with 8VFS|1|A|G|13
pMakeNodesProbeForInsertions:  B 8VFS|1|B|C|17 interacts with 8VFS|1|A|G|13
pMakeNodes probed for insert:  a=8VFS|1|A|G|13 B=8VFS|1|B|C|17
  3 Basepair    13   17 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8VFS|1|A|A|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'U'
               Comment: ' // Basepair A11 - U18 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8VFS|1|A|A|12'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G13 - C17 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_31462.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.0552
   -2.6149
   -3.0552
   -3.9639
   -2.6149
   -2.2676
   -4.5193
   -3.9639
   -2.6166
   -2.6149
   -3.7814
   -3.3004
   -3.4239
   -4.5193
   -3.3004
   -3.3004
   -3.3004
   -3.0552
   -3.7712
   -3.0552
   -3.3004
   -2.2676
   -2.6166
   -4.4347
   -3.4449
   -3.4449
   -2.2676
   -3.0552
   -5.6474
   -2.6149
   -2.2676
   -2.6149
   -2.6166
   -2.6149
   -2.6166
   -3.9639
   -2.6149
   -3.2783
   -2.6149
   -2.6149
   -2.2676
   -2.2676
   -3.2783
   -2.2676
   -3.8836
   -2.6166
   -4.1720
   -3.3004
   -2.6166
   -3.0552
   -3.0959
   -3.0959
   -3.8836
   -4.1720
   -2.2676
   -2.9531
   -4.7929
   -3.0959
   -2.6166
   -2.6149
   -3.2783
   -3.4025
   -4.7929
   -2.2676
   -2.6149
   -4.7929
   -2.6149
   -3.8836
   -2.6166
   -3.0959
   -2.9639
   -2.2676
   -3.2783
   -3.4239
   -2.2676
   -2.6149
   -3.0959
   -2.9639
   -2.6149
   -4.5193
   -2.6166
   -3.4449
   -3.7712
   -3.4239
   -3.0959
   -2.6166
   -2.2676
   -2.6166
   -2.2676
   -2.2676
   -2.6149
   -2.9531
   -2.9639
   -3.0552
   -3.0552
   -3.4239
   -2.2676
   -3.4239
   -3.7814
   -3.7712
   -3.8836
   -2.2676
   -3.2783
   -2.6166
   -3.4239
   -2.6166
   -3.6273
   -2.6149
   -2.9531
   -2.6166
   -2.6166
   -2.6166
   -2.6149
   -3.4449
   -2.2676
   -2.2676
   -4.5193
   -2.2676
   -2.6166
   -3.3004
   -2.9639
   -3.4239
   -2.6166
   -3.4239
   -3.4239
   -3.7712
   -2.6166
   -2.9531
   -2.6166
   -3.7712

Timestamp 18-Jul-2025 22:47:30
pMakeSCFGModels: Making JAR3D model for motif group IL_31504.1, number 130 of 411
pMakeNodes starting loop:     a=4V9F|1|0|G|501 B=4V9F|1|0|C|491
  2 Basepair   501  491 GC cWW 
No need to probe because of interaction between a=4V9F|1|0|A|502 B=4V9F|1|0|C|490
  3 Basepair   502  490 AC cWW 
No need to probe because of interaction between a=4V9F|1|0|G|503 B=4V9F|1|0|A|489
pMakeNodes making a cluster near strand break a=4V9F|1|0|G|503 B=4V9F|1|0|A|489
pMakeNodesCluster: amax is 13 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 13 and then 14 to 16
aa is 13 bb is 14
  4 Cluster   4V9F|1|0|G|503:4V9F|1|0|C|515 4V9F|1|0|G|487:4V9F|1|0|A|489
    LR Inter  4V9F|1|0|G|512 4V9F|1|0|G|487 tSS 
    LR Inter  4V9F|1|0|C|515 4V9F|1|0|G|487 cWW 
    LR Inter  4V9F|1|0|G|503 4V9F|1|0|U|488 cWS 
    LR Inter  4V9F|1|0|A|513 4V9F|1|0|U|488 tHH 
    LR Inter  4V9F|1|0|G|503 4V9F|1|0|A|489 tSH 
    LL Inter  4V9F|1|0|C|505 4V9F|1|0|A|509 tWH 
    LL Inter  4V9F|1|0|G|506 4V9F|1|0|A|511 tSH 
    LL Inter  4V9F|1|0|G|504 4V9F|1|0|G|512 bif 
    Left  strand conserved insertion 4V9F|1|0|A|507 at position 5
    Left  strand conserved insertion 4V9F|1|0|A|508 at position 6
pMakeNodesCluster a=14 B=13 at the end
pMakeNodesCluster a=14 B=13 at the end
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6  7  8  9 10 11 12 13 Right 14 15 16
pMakeMotifModelFromSSF:   5   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G501 - C491 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A502 - C490 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4 5 6 7 8 9 10 11 12 13]
            RightIndex: [14 15 16]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGCGAAAAGAC'
           RightLetter: 'GUA'
               Comment: ' // Cluster node 4V9F|1|0|G|503:4V9F|1|0|C|515 and 4V9F|1|0|G|487:4V9F|1|0|A|489'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×10 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8 9 10 11]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [10×2 double]
    InteractionComment: {1×10 cell}
      JunctionDeletion: []
          InterIndices: [10×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [5 6]
         RightNotInter: [1×0 double]
              NormCons: 0.0084

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 14
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 14
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 14
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6  7  8  9 10 11 12 13 Right 14 15 16
pMakeMotifModelFromSSF:   5   Initial Left 14 Right 13
pMakeMotifModelFromSSF:   6   Hairpin Left 14 Right 13
pNextNodeJunction: Found a hairpin at node 6
pUpdateModelWithSSF: IL_31504.1 allow insertions from initial node 5?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_31504.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.5589

Timestamp 18-Jul-2025 22:47:30
pMakeSCFGModels: Making JAR3D model for motif group IL_31531.3, number 131 of 411
pMakeNodes starting loop:     a=2ET8|1|B|G|38 B=2ET8|1|A|C|8
  2 Basepair    38    8 GC cWW 
pMakeNodes probe for inserts:  a=2ET8|1|B|A|39 B=2ET8|1|A|A|7
    Insertion on left  2ET8|1|B|A|39
    Insertion on left  2ET8|1|B|A|40
    Insertion on right 2ET8|1|A|A|7
pMakeNodesProbeForInsertions:  a 2ET8|1|B|G|41 interacts with 2ET8|1|A|C|6
pMakeNodesProbeForInsertions:  B 2ET8|1|A|C|6 interacts with 2ET8|1|B|G|41
pMakeNodesProbeForInsertions:  B 2ET8|1|A|C|6 interacts with 2ET8|1|B|G|41
pMakeNodes probed for insert:  a=2ET8|1|B|G|41 B=2ET8|1|A|C|6
  3 Basepair    41    6 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2ET8|1|A|A|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2ET8|1|A|C|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 2ET8|1|B|A|40
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAA'
           RightLetter: 'AC'
               Comment: ' // Basepair G38 - C8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2ET8|1|A|A|7'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2ET8|1|A|C|8'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 2ET8|1|B|A|40'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G41 - C6 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_31531.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.4261
   -3.4261
   -5.3435
   -3.4261
   -3.4261
   -3.4261
   -3.4261
   -3.4261
   -6.6962
   -3.4261
   -4.3735
   -5.8996
   -4.3735

Timestamp 18-Jul-2025 22:47:31
pMakeSCFGModels: Making JAR3D model for motif group IL_31558.1, number 132 of 411
pMakeNodes starting loop:     a=6JXM|1|B|C|35 B=6JXM|1|B|G|53
  2 Basepair    35   53 CG cWW 
pMakeNodes probe for inserts:  a=6JXM|1|B|G|36 B=6JXM|1|B|G|52
    Insertion on left  6JXM|1|B|G|36
    Insertion on left  6JXM|1|B|A|37
pMakeNodesProbeForInsertions:  a 6JXM|1|B|A|38 interacts with 6JXM|1|B|G|52
pMakeNodesProbeForInsertions:  B 6JXM|1|B|G|52 interacts with 6JXM|1|B|A|38
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6JXM|1|B|G|52 interacts with 6JXM|1|B|A|38
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6JXM|1|B|A|38 B=6JXM|1|B|G|52
  3 Basepair    38   52 AG tHS 
pMakeNodes probe for inserts:  a=6JXM|1|B|G|39 B=6JXM|1|B|G|51
    Insertion on right 6JXM|1|B|G|51
pMakeNodesProbeForInsertions:  a 6JXM|1|B|G|39 interacts with 6JXM|1|B|U|50
pMakeNodesProbeForInsertions:  B 6JXM|1|B|U|50 interacts with 6JXM|1|B|G|39
pMakeNodesProbeForInsertions:  B 6JXM|1|B|U|50 interacts with 6JXM|1|B|G|39
pMakeNodes probed for insert:  a=6JXM|1|B|G|39 B=6JXM|1|B|U|50
  4 Basepair    39   50 GU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6JXM|1|B|G|36
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6JXM|1|B|A|37
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6JXM|1|B|G|51
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGA'
           RightLetter: 'G'
               Comment: ' // Basepair C35 - G53 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6JXM|1|B|G|36'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6JXM|1|B|A|37'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'GG'
               Comment: ' // Basepair A38 - G52 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6JXM|1|B|G|51'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G39 - U50 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_31558.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7275

Timestamp 18-Jul-2025 22:47:31
pMakeSCFGModels: Making JAR3D model for motif group IL_31561.1, number 133 of 411
pMakeNodes starting loop:     a=4LFB|1|A|G|477 B=4LFB|1|A|C|455
  2 Basepair   477  455 GC cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|A|478 B=4LFB|1|A|C|454
    Insertion on left  4LFB|1|A|A|478
    Insertion on right 4LFB|1|A|C|454
pMakeNodesProbeForInsertions:  a 4LFB|1|A|C|479 interacts with 4LFB|1|A|A|453
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|453 interacts with 4LFB|1|A|C|479
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|453 interacts with 4LFB|1|A|C|479
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4LFB|1|A|C|479 B=4LFB|1|A|A|453
  3 Basepair   479  453 CA tWH 
No need to probe because of interaction between a=4LFB|1|A|U|480 B=4LFB|1|A|A|452
  4 Basepair   480  452 UA tWH 
pMakeNodes probe for inserts:  a=4LFB|1|A|G|481 B=4LFB|1|A|A|451
    Insertion on left  4LFB|1|A|G|481
    Insertion on left  4LFB|1|A|A|482
    Insertion on right 4LFB|1|A|A|451
pMakeNodesProbeForInsertions:  a 4LFB|1|A|C|483 interacts with 4LFB|1|A|G|450
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|450 interacts with 4LFB|1|A|C|483
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|450 interacts with 4LFB|1|A|C|483
pMakeNodes probed for insert:  a=4LFB|1|A|C|483 B=4LFB|1|A|G|450
  5 Basepair   483  450 CG cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|451
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|A|482
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|C|454
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|C|455
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|C|479
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'CC'
               Comment: ' // Basepair G477 - C455 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|451'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'UGA'
           RightLetter: 'AA'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|A|482'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C479 - A453 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGA'
           RightLetter: 'AA'
               Comment: ' // Basepair U480 - A452 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|C|454'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|C|455'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|C|479'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C483 - G450 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 19
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  9
pMakeMotifModelFromSSF:  12   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  14   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  15  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  16   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a hairpin at node 16

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_31561.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.5778

Timestamp 18-Jul-2025 22:47:31
pMakeSCFGModels: Making JAR3D model for motif group IL_31737.3, number 134 of 411
pMakeNodes starting loop:     a=2ET8|1|B|G|41 B=2ET8|1|A|C|6
  2 Basepair    41    6 GC cWW 
pMakeNodes probe for inserts:  a=2ET8|1|B|U|42 B=2ET8|1|A|G|4
    Insertion on left  2ET8|1|B|U|42
pMakeNodesProbeForInsertions:  a 2ET8|1|B|C|43 interacts with 2ET8|1|A|G|4
pMakeNodesProbeForInsertions:  B 2ET8|1|A|G|4 interacts with 2ET8|1|B|C|43
pMakeNodesProbeForInsertions:  B 2ET8|1|A|G|4 interacts with 2ET8|1|B|C|43
pMakeNodes probed for insert:  a=2ET8|1|B|C|43 B=2ET8|1|A|G|4
  3 Basepair    43    4 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2ET8|1|A|U|5
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GU'
           RightLetter: 'C'
               Comment: ' // Basepair G41 - C6 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2ET8|1|A|U|5'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C43 - G4 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_31737.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7199
   -6.7199
   -6.3045
   -6.1452
   -7.6126
   -6.2740
   -6.0540
   -4.8320
   -4.8320
   -9.0071
   -6.2740
  -12.0198

Timestamp 18-Jul-2025 22:47:32
pMakeSCFGModels: Making JAR3D model for motif group IL_31915.1, number 135 of 411
pMakeNodes starting loop:     a=3P22|1|A|G|26 B=3P22|1|A|C|13
  2 Basepair    26   13 GC cWW 
pMakeNodes probe for inserts:  a=3P22|1|A|U|27 B=3P22|1|A|U|12
    Insertion on left  3P22|1|A|U|27
    Insertion on left  3P22|1|A|U|28
    Insertion on left  3P22|1|A|U|29
    Insertion on left  3P22|1|A|U|30
    Insertion on left  3P22|1|A|U|31
    Insertion on left  3P22|1|A|U|33
    Insertion on right 3P22|1|A|U|12
    Insertion on right 3P22|1|A|U|11
    Insertion on right 3P22|1|A|U|10
    Insertion on right 3P22|1|A|U|9
    Insertion on right 3P22|1|A|U|8
pMakeNodesProbeForInsertions:  a 3P22|1|A|C|34 interacts with 3P22|1|A|G|7
pMakeNodesProbeForInsertions:  B 3P22|1|A|G|7 interacts with 3P22|1|A|C|34
pMakeNodesProbeForInsertions:  B 3P22|1|A|G|7 interacts with 3P22|1|A|C|34
pMakeNodes probed for insert:  a=3P22|1|A|C|34 B=3P22|1|A|G|7
  3 Basepair    34    7 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   4   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3P22|1|A|U|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3P22|1|A|U|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3P22|1|A|U|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3P22|1|A|U|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3P22|1|A|U|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3P22|1|A|C|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3P22|1|A|A|32
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3P22|1|A|U|31
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3P22|1|A|U|30
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3P22|1|A|U|29
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3P22|1|A|U|28
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUUUUUU'
           RightLetter: 'UUUUUC'
               Comment: ' // Basepair G26 - C13 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3P22|1|A|U|8'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3P22|1|A|U|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                  rpar: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3P22|1|A|U|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                  lpar: []
                  rpar: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3P22|1|A|U|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3P22|1|A|U|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                IBases: []
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                  rpar: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3P22|1|A|C|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3P22|1|A|A|32'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3P22|1|A|U|31'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 8
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 8
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3P22|1|A|U|30'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3P22|1|A|U|29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3P22|1|A|U|28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 26
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C34 - G7 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 28
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 14
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 14
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 14
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 14
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 14
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 14
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 14
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 14
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 14
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 14
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 14
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 13
pMakeMotifModelFromSSF:  17     Fixed Left  8 Right 13
pMakeMotifModelFromSSF:  18   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  19     Fixed Left  8 Right 12
pMakeMotifModelFromSSF:  20   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  21     Fixed Left  8 Right 11
pMakeMotifModelFromSSF:  22   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  23     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  24   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  25  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  26   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 26
pNextNodeJunction: Found a hairpin at node 26

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_31915.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.5073
   -8.5073
   -9.7276

Timestamp 18-Jul-2025 22:47:32
pMakeSCFGModels: Making JAR3D model for motif group IL_32016.1, number 136 of 411
pMakeNodes starting loop:     a=4V9F|1|0|U|1587 B=4V9F|1|0|G|1608
  2 Basepair  1587 1608 UG cWW 
No need to probe because of interaction between a=4V9F|1|0|G|1588 B=4V9F|1|0|A|1607
  3 Basepair  1588 1607 GA tSH 
No need to probe because of interaction between a=4V9F|1|0|G|1589 B=4V9F|1|0|A|1606
  4 Basepair  1589 1606 GA tSH 
No need to probe because of interaction between a=4V9F|1|0|A|1590 B=4V9F|1|0|G|1605
pMakeNodes making a cluster near strand break a=4V9F|1|0|A|1590 B=4V9F|1|0|G|1605
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 6 and then 7 to 9
aa is 6 bb is 7
  5 Cluster   4V9F|1|0|A|1590:4V9F|1|0|G|1592 4V9F|1|0|C|1602:4V9F|1|0|G|1605
    LR Inter  4V9F|1|0|A|1590 4V9F|1|0|C|1602 tSS 
    LR Inter  4V9F|1|0|G|1592 4V9F|1|0|C|1602 cWW 
    LR Inter  4V9F|1|0|A|1590 4V9F|1|0|G|1605 tHS 
    Left  strand conserved insertion 4V9F|1|0|A|1591 at position 2
    Right strand conserved insertion 4V9F|1|0|A|1603 at position 2
pMakeNodesCluster a=7 B=6 at the end
pMakeNodesCluster a=7 B=6 at the end
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5   Cluster Left  4  5  6 Right  7  8  9
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U1587 - G1608 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1588 - A1607 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1589 - A1606 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [4 5 6]
            RightIndex: [7 8 9]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAG'
           RightLetter: 'CAG'
               Comment: ' // Cluster node 4V9F|1|0|A|1590:4V9F|1|0|G|1592 and 4V9F|1|0|C|1602:4V9F|1|0|G|1605'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: 2
              NormCons: 0.0993

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5   Cluster Left  4  5  6 Right  7  8  9
pMakeMotifModelFromSSF:   6   Initial Left  7 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 7
pUpdateModelWithSSF: IL_32016.1 allow insertions from initial node 6?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_32016.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1551

Timestamp 18-Jul-2025 22:47:33
pMakeSCFGModels: Making JAR3D model for motif group IL_32056.1, number 137 of 411
pMakeNodes starting loop:     a=5ML7|1|B|G|2151 B=5ML7|1|B|C|2224
  2 Basepair  2151 2224 GC cWW 
pMakeNodes probe for inserts:  a=5ML7|1|B|U|2152 B=5ML7|1|B|C|2223
    Insertion on left  5ML7|1|B|U|2152
    Insertion on left  5ML7|1|B|G|2153
    Insertion on left  5ML7|1|B|C|2154
pMakeNodesProbeForInsertions:  a 5ML7|1|B|A|2155 interacts with 5ML7|1|B|A|2160
pMakeNodesProbeForInsertions:  B 5ML7|1|B|C|2223 interacts with 5ML7|1|B|G|2161
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 5ML7|1|B|C|2223 interacts with 5ML7|1|B|G|2161
pMakeNodes probed for insert:  a=5ML7|1|B|A|2155 B=5ML7|1|B|C|2223
pMakeNodes making a cluster near strand break a=5ML7|1|B|A|2155 B=5ML7|1|B|C|2223
pMakeNodesCluster: amax is 11 bmin is 12, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 11 and then 12 to 12
aa is 11 bb is 12
  3 Cluster   5ML7|1|B|A|2155:5ML7|1|B|G|2161 5ML7|1|B|C|2223:5ML7|1|B|C|2223
    LR Inter  5ML7|1|B|G|2161 5ML7|1|B|C|2223 cWW 
    LL Inter  5ML7|1|B|A|2155 5ML7|1|B|A|2160 tWH 
    Left  strand conserved insertion 5ML7|1|B|G|2156 at position 2
    Left  strand conserved insertion 5ML7|1|B|C|2157 at position 3
    Left  strand conserved insertion 5ML7|1|B|A|2158 at position 4
    Left  strand conserved insertion 5ML7|1|B|U|2159 at position 5
pMakeNodesCluster a=12 B=11 at the end
pMakeNodesCluster a=12 B=11 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  5  6  7  8  9 10 11 Right 12
pMakeMotifModelFromSSF:   4   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5ML7|1|B|U|2152
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5ML7|1|B|G|2153
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5ML7|1|B|C|2154
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 0 0 0 0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUGC'
           RightLetter: 'C'
               Comment: ' // Basepair G2151 - C2224 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5ML7|1|B|U|2152'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4 5]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5ML7|1|B|G|2153'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5ML7|1|B|C|2154'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 10
             LeftIndex: [5 6 7 8 9 10 11]
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGCAUAG'
           RightLetter: 'C'
               Comment: ' // Cluster node 5ML7|1|B|A|2155:5ML7|1|B|G|2161 and 5ML7|1|B|C|2223:5ML7|1|B|C|2223'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4 5]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 12
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 12
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9   Cluster Left  5  6  7  8  9 10 11 Right 12
pMakeMotifModelFromSSF:  10   Initial Left 12 Right 11
pMakeMotifModelFromSSF:  11   Hairpin Left 12 Right 11
pNextNodeJunction: Found a hairpin at node 11
pUpdateModelWithSSF: IL_32056.1 allow insertions from initial node 10?
ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_32056.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0899
   -6.5574
   -6.5574

Timestamp 18-Jul-2025 22:47:33
pMakeSCFGModels: Making JAR3D model for motif group IL_33141.1, number 138 of 411
pMakeNodes starting loop:     a=8DK7|1|C|C|21 B=8DK7|1|C|G|11
  2 Basepair    21   11 CG cWW 
No need to probe because of interaction between a=8DK7|1|C|C|22 B=8DK7|1|C|A|10
  3 Basepair    22   10 CA bif 
pMakeNodes probe for inserts:  a=8DK7|1|C|C|23 B=8DK7|1|C|C|9
    Insertion on left  8DK7|1|C|C|23
    Insertion on left  8DK7|1|C|U|24
    Insertion on left  8DK7|1|C|U|25
pMakeNodesProbeForInsertions:  a 8DK7|1|C|G|26 interacts with 8DK7|1|C|C|9
pMakeNodesProbeForInsertions:  B 8DK7|1|C|C|9 interacts with 8DK7|1|C|G|26
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8DK7|1|C|C|9 interacts with 8DK7|1|C|G|26
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8DK7|1|C|G|26 B=8DK7|1|C|C|9
  4 Basepair    26    9 GC cWW 
No need to probe because of interaction between a=8DK7|1|C|G|27 B=8DK7|1|C|C|8
  5 Basepair    27    8 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8DK7|1|C|A|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8DK7|1|C|G|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8DK7|1|C|C|21
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C21 - G11 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CCUU'
           RightLetter: 'A'
               Comment: ' // Basepair C22 - A10 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8DK7|1|C|A|10'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8DK7|1|C|G|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8DK7|1|C|C|21'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G26 - C9 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G27 - C8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  12   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_33141.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.0559

Timestamp 18-Jul-2025 22:47:34
pMakeSCFGModels: Making JAR3D model for motif group IL_33323.1, number 139 of 411
pMakeNodes starting loop:     a=8D28|1|B|C|20 B=8D28|1|B|G|11
  2 Basepair    20   11 CG cWW 
No need to probe because of interaction between a=8D28|1|B|C|21 B=8D28|1|B|A|10
  3 Basepair    21   10 CA cWW 
pMakeNodes probe for inserts:  a=8D28|1|B|C|22 B=8D28|1|B|C|9
pMakeNodesProbeForInsertions:  a 8D28|1|B|C|22 interacts with 8D28|1|B|G|25
pMakeNodesProbeForInsertions:  B 8D28|1|B|C|9 interacts with 8D28|1|B|G|25
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8D28|1|B|C|9 interacts with 8D28|1|B|G|25
pMakeNodes probed for insert:  a=8D28|1|B|C|22 B=8D28|1|B|C|9
pMakeNodes making a cluster near strand break a=8D28|1|B|C|22 B=8D28|1|B|C|9
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 6 and then 7 to 7
aa is 6 bb is 7
  4 Cluster   8D28|1|B|C|22:8D28|1|B|G|25 8D28|1|B|C|9:8D28|1|B|C|9
    LR Inter  8D28|1|B|G|25 8D28|1|B|C|9 cWW 
    LL Inter  8D28|1|B|C|22 8D28|1|B|G|25 cSH 
    Left  strand conserved insertion 8D28|1|B|U|23 at position 2
    Left  strand conserved insertion 8D28|1|B|U|24 at position 3
pMakeNodesCluster a=7 B=6 at the end
pMakeNodesCluster a=7 B=6 at the end
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C20 - G11 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C21 - A10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4 5 6]
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUUG'
           RightLetter: 'C'
               Comment: ' // Cluster node 8D28|1|B|C|22:8D28|1|B|G|25 and 8D28|1|B|C|9:8D28|1|B|C|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.2532

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6 Right  7
pMakeMotifModelFromSSF:   5   Initial Left  7 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 6
pUpdateModelWithSSF: IL_33323.1 allow insertions from initial node 5?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_33323.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.1135
   -6.4717

Timestamp 18-Jul-2025 22:47:34
pMakeSCFGModels: Making JAR3D model for motif group IL_33623.1, number 140 of 411
pMakeNodes starting loop:     a=5T83|1|A|C|69 B=5T83|1|A|G|89
  2 Basepair    69   89 CG cWW 
pMakeNodes probe for inserts:  a=5T83|1|A|A|70 B=5T83|1|A|G|88
    Insertion on left  5T83|1|A|A|70
    Insertion on left  5T83|1|A|C|71
    Insertion on left  5T83|1|A|G|72
    Insertion on left  5T83|1|A|G|73
pMakeNodesProbeForInsertions:  a 5T83|1|A|A|74 interacts with 5T83|1|A|G|88
pMakeNodesProbeForInsertions:  B 5T83|1|A|G|88 interacts with 5T83|1|A|A|74
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5T83|1|A|G|88 interacts with 5T83|1|A|A|74
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5T83|1|A|A|74 B=5T83|1|A|G|88
  3 Basepair    74   88 AG tHH 
No need to probe because of interaction between a=5T83|1|A|A|75 B=5T83|1|A|U|87
  4 Basepair    75   87 AU cWS 
No need to probe because of interaction between a=5T83|1|A|G|76 B=5T83|1|A|C|86
  5 Basepair    76   86 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   6   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5T83|1|A|A|70
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5T83|1|A|C|71
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5T83|1|A|G|72
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5T83|1|A|G|73
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CACGG'
           RightLetter: 'G'
               Comment: ' // Basepair C69 - G89 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5T83|1|A|A|70'
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5T83|1|A|C|71'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5T83|1|A|G|72'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5T83|1|A|G|73'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A74 - G88 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A75 - U87 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G76 - C86 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:  12  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  14   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_33623.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.9288

Timestamp 18-Jul-2025 22:47:34
pMakeSCFGModels: Making JAR3D model for motif group IL_33711.1, number 141 of 411
pMakeNodes starting loop:     a=6N2V|1|A|A|45 B=6N2V|1|A|U|65
pMakeNodes making a cluster near strand break a=6N2V|1|A|A|45 B=6N2V|1|A|U|65
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 9 to 9
aa is 2 bb is 9
  2 Cluster   6N2V|1|A|A|45:6N2V|1|A|A|46 6N2V|1|A|U|65:6N2V|1|A|U|65
    LR Inter  6N2V|1|A|A|45 6N2V|1|A|U|65 cWW 
    LL Inter  6N2V|1|A|A|45 6N2V|1|A|A|46 cSH 
pMakeNodesCluster a=3 B=8 at the end
pMakeNodesCluster a=3 B=8 at the end
pMakeNodes probe for inserts:  a=6N2V|1|A|C|47 B=6N2V|1|A|G|64
    Insertion on left  6N2V|1|A|C|47
    Insertion on left  6N2V|1|A|A|48
    Insertion on left  6N2V|1|A|C|51
    Insertion on left  6N2V|1|A|U|52
pMakeNodesProbeForInsertions:  a 6N2V|1|A|C|53 interacts with 6N2V|1|A|G|64
pMakeNodesProbeForInsertions:  B 6N2V|1|A|G|64 interacts with 6N2V|1|A|C|53
pMakeNodesProbeForInsertions:  B 6N2V|1|A|G|64 interacts with 6N2V|1|A|C|53
  3 Initial     47 (4 insertion) and   64 (0 insertion)
pMakeNodes probed for insert:  a=6N2V|1|A|C|53 B=6N2V|1|A|G|64
  4 Basepair    53   64 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  9
pMakeMotifModelFromSSF:   3   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N2V|1|A|C|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N2V|1|A|A|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N2V|1|A|U|49
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N2V|1|A|A|50
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AA'
           RightLetter: 'U'
               Comment: ' // Cluster node 6N2V|1|A|A|45:6N2V|1|A|A|46 and 6N2V|1|A|U|65:6N2V|1|A|U|65'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2494
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CACU'
           RightLetter: []
               Comment: ' // Initial node 6N2V|1|A|C|47 - 6N2V|1|A|G|64 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6N2V|1|A|C|47'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6N2V|1|A|A|48'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6N2V|1|A|U|49'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6N2V|1|A|A|50'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C53 - G64 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  9
pMakeMotifModelFromSSF:   3   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  11   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  12  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  13   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_33711.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0055
   -8.0233

Timestamp 18-Jul-2025 22:47:35
pMakeSCFGModels: Making JAR3D model for motif group IL_33761.2, number 142 of 411
pMakeNodes starting loop:     a=4LFB|1|A|U|129 B=4LFB|1|A|G|232
  2 Basepair   129  232 UG cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|A|130 B=4LFB|1|A|G|231
    Insertion on left  4LFB|1|A|A|130
pMakeNodesProbeForInsertions:  a 4LFB|1|A|C|131 interacts with 4LFB|1|A|G|231
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|231 interacts with 4LFB|1|A|C|131
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|231 interacts with 4LFB|1|A|C|131
pMakeNodes probed for insert:  a=4LFB|1|A|C|131 B=4LFB|1|A|G|231
  3 Basepair   131  231 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|129|||A
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: 'G'
               Comment: ' // Basepair U129 - G232 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|G|129|||A'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C131 - G231 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_33761.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.3180
   -4.3130
   -3.7914

Timestamp 18-Jul-2025 22:47:35
pMakeSCFGModels: Making JAR3D model for motif group IL_33886.1, number 143 of 411
pMakeNodes starting loop:     a=4V9F|1|0|C|260 B=4V9F|1|0|G|249
  2 Basepair   260  249 CG cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|261 B=4V9F|1|0|A|248
    Insertion on left  4V9F|1|0|A|261
    Insertion on left  4V9F|1|0|A|262
pMakeNodesProbeForInsertions:  a 4V9F|1|0|G|264 interacts with 4V9F|1|0|A|247
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|248 interacts with 4V9F|1|0|U|265
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|248 interacts with 4V9F|1|0|U|265
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4V9F|1|0|G|264 B=4V9F|1|0|A|248
pMakeNodes making a cluster near strand break a=4V9F|1|0|G|264 B=4V9F|1|0|A|248
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 8 to 10
aa is 5 bb is 8
  3 Cluster   4V9F|1|0|G|264:4V9F|1|0|U|265 4V9F|1|0|G|246:4V9F|1|0|A|248
    LR Inter  4V9F|1|0|U|265 4V9F|1|0|G|246 tHS 
    LR Inter  4V9F|1|0|G|264 4V9F|1|0|A|247 tSH 
    LR Inter  4V9F|1|0|U|265 4V9F|1|0|A|248 cWW 
    LL Inter  4V9F|1|0|G|264 4V9F|1|0|U|265 cSH 
pMakeNodesCluster a=6 B=7 at the end
pMakeNodesCluster a=6 B=7 at the end
No need to probe because of interaction between a=4V9F|1|0|G|266 B=4V9F|1|0|C|245
  4 Basepair   266  245 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  4  5 Right  8  9 10
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|G|246
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|247
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAA'
           RightLetter: 'G'
               Comment: ' // Basepair C260 - G249 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|G|246'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0189

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|A|247'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [4 5]
            RightIndex: [8 9 10]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'GAA'
               Comment: ' // Cluster node 4V9F|1|0|G|264:4V9F|1|0|U|265 and 4V9F|1|0|G|246:4V9F|1|0|A|248'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0189

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G266 - C245 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7   Cluster Left  4  5 Right  8  9 10
pMakeMotifModelFromSSF:   8   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  10   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_33886.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.9225
  -10.9481

Timestamp 18-Jul-2025 22:47:35
pMakeSCFGModels: Making JAR3D model for motif group IL_34470.3, number 144 of 411
pMakeNodes starting loop:     a=3DIL|1|A|G|22 B=3DIL|1|A|C|70
  2 Basepair    22   70 GC cWW 
No need to probe because of interaction between a=3DIL|1|A|A|23 B=3DIL|1|A|G|69
  3 Basepair    23   69 AG cWW 
pMakeNodes probe for inserts:  a=3DIL|1|A|U|24 B=3DIL|1|A|G|68
    Insertion on left  3DIL|1|A|U|24
    Insertion on right 3DIL|1|A|G|68
pMakeNodesProbeForInsertions:  a 3DIL|1|A|G|25 interacts with 3DIL|1|A|A|67
pMakeNodesProbeForInsertions:  B 3DIL|1|A|A|67 interacts with 3DIL|1|A|G|25
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3DIL|1|A|A|67 interacts with 3DIL|1|A|G|25
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3DIL|1|A|G|25 B=3DIL|1|A|A|67
  4 Basepair    25   67 GA tSH 
No need to probe because of interaction between a=3DIL|1|A|A|26 B=3DIL|1|A|A|66
  5 Basepair    26   66 AA tHH 
pMakeNodes probe for inserts:  a=3DIL|1|A|G|27 B=3DIL|1|A|A|65
pMakeNodesProbeForInsertions:  a 3DIL|1|A|G|27 interacts with 3DIL|1|A|U|28
pMakeNodesProbeForInsertions:  B 3DIL|1|A|A|65 interacts with 3DIL|1|A|U|28
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 3DIL|1|A|A|65 interacts with 3DIL|1|A|U|28
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3DIL|1|A|G|27 B=3DIL|1|A|A|65
pMakeNodes making a cluster near strand break a=3DIL|1|A|G|27 B=3DIL|1|A|A|65
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 6 to 7 and then 12 to 12
aa is 7 bb is 12
  6 Cluster   3DIL|1|A|G|27:3DIL|1|A|U|28 3DIL|1|A|A|65:3DIL|1|A|A|65
    LR Inter  3DIL|1|A|U|28 3DIL|1|A|A|65 tWH 
    LL Inter  3DIL|1|A|G|27 3DIL|1|A|U|28 cSH 
pMakeNodesCluster a=8 B=11 at the end
pMakeNodesCluster a=8 B=11 at the end
No need to probe because of interaction between a=3DIL|1|A|A|29 B=3DIL|1|A|G|64
  7 Basepair    29   64 AG tHS 
No need to probe because of interaction between a=3DIL|1|A|G|30 B=3DIL|1|A|U|63
  8 Basepair    30   63 GU cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right 14
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right 13
pMakeMotifModelFromSSF:   6   Cluster Left  6  7 Right 12
pMakeMotifModelFromSSF:   7  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:   8  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   9   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3DIL|1|A|U|24
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3DIL|1|A|G|68
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [17×17 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G22 - C70 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AU'
           RightLetter: 'GG'
               Comment: ' // Basepair A23 - G69 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3DIL|1|A|U|24'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3DIL|1|A|G|68'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G25 - A67 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A26 - A66 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 11
             LeftIndex: [6 7]
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 3DIL|1|A|G|27:3DIL|1|A|U|28 and 3DIL|1|A|A|65:3DIL|1|A|A|65'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A29 - G64 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G30 - U63 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 15
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 15
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 14
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right 14
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right 13
pMakeMotifModelFromSSF:  10   Cluster Left  6  7 Right 12
pMakeMotifModelFromSSF:  11   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  12  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  14   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_34470.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.9642
   -8.9642

Timestamp 18-Jul-2025 22:47:36
pMakeSCFGModels: Making JAR3D model for motif group IL_34737.1, number 145 of 411
pMakeNodes starting loop:     a=8CRE|1|1|C|973 B=8CRE|1|1|G|1100
  2 Basepair   973 1100 CG cWW 
pMakeNodes probe for inserts:  a=8CRE|1|1|G|974 B=8CRE|1|1|A|1098
    Insertion on left  8CRE|1|1|G|974
    Insertion on left  8CRE|1|1|U|975
    Insertion on left  8CRE|1|1|A|976
pMakeNodesProbeForInsertions:  a 8CRE|1|1|U|977 interacts with 8CRE|1|1|A|1098
pMakeNodesProbeForInsertions:  B 8CRE|1|1|A|1098 interacts with 8CRE|1|1|U|977
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8CRE|1|1|A|1098 interacts with 8CRE|1|1|U|977
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8CRE|1|1|U|977 B=8CRE|1|1|A|1098
  3 Basepair   977 1098 UA cHW 
No need to probe because of interaction between a=8CRE|1|1|C|978 B=8CRE|1|1|G|1097
  4 Basepair   978 1097 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|G|974
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|U|975
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|A|976
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGUA'
           RightLetter: 'G'
               Comment: ' // Basepair C973 - G1100 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|G|974'
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|U|975'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|A|976'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U977 - A1098 cHW '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C978 - G1097 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_34737.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4607

Timestamp 18-Jul-2025 22:47:36
pMakeSCFGModels: Making JAR3D model for motif group IL_34739.3, number 146 of 411
pMakeNodes starting loop:     a=4N0T|1|B|G|39 B=4N0T|1|B|C|92
pMakeNodes making a cluster near strand break a=4N0T|1|B|G|39 B=4N0T|1|B|C|92
pMakeNodesCluster: amax is 15 bmin is 16, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 19 to 20
aa is 2 bb is 19
  2 Cluster   4N0T|1|B|G|39:4N0T|1|B|A|40 4N0T|1|B|A|91:4N0T|1|B|C|92
    LR Inter  4N0T|1|B|A|40 4N0T|1|B|A|91 tWW 
    LR Inter  4N0T|1|B|G|39 4N0T|1|B|C|92 cWW 
    LR Inter  4N0T|1|B|A|40 4N0T|1|B|C|92 tWW 
pMakeNodesCluster a=3 B=18 at the end
pMakeNodesCluster a=3 B=18 at the end
pMakeNodes probe for inserts:  a=4N0T|1|B|A|41 B=4N0T|1|B|U|90
    Insertion on left  4N0T|1|B|A|41
    Insertion on left  4N0T|1|B|C|43
    Insertion on left  4N0T|1|B|A|44
    Insertion on left  4N0T|1|B|A|45
    Insertion on left  4N0T|1|B|U|46
    Insertion on left  4N0T|1|B|A|47
    Insertion on left  4N0T|1|B|C|48
    Insertion on left  4N0T|1|B|G|50
    Insertion on left  4N0T|1|B|A|51
    Insertion on left  4N0T|1|B|G|52
    Insertion on left  4N0T|1|B|A|53
    Insertion on left  4N0T|1|B|A|56
    Insertion on right 4N0T|1|B|U|90
    Insertion on right 4N0T|1|B|U|89
pMakeNodesProbeForInsertions:  a 4N0T|1|B|A|59 interacts with 4N0T|1|B|U|88
pMakeNodesProbeForInsertions:  B 4N0T|1|B|U|88 interacts with 4N0T|1|B|A|59
pMakeNodesProbeForInsertions:  B 4N0T|1|B|U|88 interacts with 4N0T|1|B|A|59
  3 Initial     41 (12 insertion) and   90 (2 insertion)
pMakeNodes probed for insert:  a=4N0T|1|B|A|59 B=4N0T|1|B|U|88
  4 Basepair    59   88 AU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 19 20
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 18
pMakeMotifModelFromSSF:   4  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:   5   Hairpin Left 16 Right 15
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|A|41
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|A|42
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|C|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|A|44
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|A|45
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|U|46
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|A|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|C|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|A|49
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|G|50
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|A|51
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|G|52
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4N0T|1|B|A|56
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4N0T|1|B|G|55
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 20
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [20×20 double]
         Extensibility: [0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: [19 20]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GA'
           RightLetter: 'AC'
               Comment: ' // Cluster node 4N0T|1|B|G|39:4N0T|1|B|A|40 and 4N0T|1|B|A|91:4N0T|1|B|C|92'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0975
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 3
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'ACAAUACGAGAA'
           RightLetter: 'UU'
               Comment: ' // Initial node 4N0T|1|B|A|41 - 4N0T|1|B|U|90 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|A|41'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 16
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|A|42'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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          LeftNotInter: []
         RightNotInter: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|C|43'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 18
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        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|A|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
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                     Z: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 18
             Insertion: []
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        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 13
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            RightIndex: 18
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        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|A|45'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
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                     Z: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 14
             LeftIndex: 8
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 15
             LeftIndex: 8
            RightIndex: 18
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        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|U|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
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                     Z: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 16
             LeftIndex: 9
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 17
             LeftIndex: 9
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        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|A|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
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                     Z: []
           MiddleIndex: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 10
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             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 19
             LeftIndex: 10
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             Insertion: []
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        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|C|48'
              NumLoops: []
                  Edge: []
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                Delete: 1.0000e-03
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                     Z: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 11
            RightIndex: 18
             Insertion: []
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        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
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                     Z: []
           MiddleIndex: []
                     P: []
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Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 21
             LeftIndex: 11
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|A|49'
              NumLoops: []
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                Delete: 1.0000e-03
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Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 22
             LeftIndex: 12
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
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                     Z: []
           MiddleIndex: []
                     P: []
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Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 23
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            RightIndex: 18
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        leftLengthDist: [0 1]
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       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|G|50'
              NumLoops: []
                  Edge: []
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                Delete: 1.0000e-03
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                     Z: []
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Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 24
             LeftIndex: 13
            RightIndex: 18
             Insertion: []
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        leftLengthDist: [0.9999 1.0000e-04]
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
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                     Z: []
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                     P: []
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Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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        leftLengthDist: [0 1]
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|A|51'
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                Delete: 1.0000e-03
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Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 26
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
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                     Z: []
           MiddleIndex: []
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Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|G|52'
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                Delete: 1.0000e-03
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                     Z: []
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Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 28
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            RightIndex: 18
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
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                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: ''
               Comment: ' // Fixed node on right for 4N0T|1|B|A|56'
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                Delete: 1.0000e-03
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Node 29

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
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         Extensibility: []
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Node 30

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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           RightLetter: ''
               Comment: ' // Fixed node on right for 4N0T|1|B|G|55'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 31

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 32
             LeftIndex: 15
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 32

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 33
             LeftIndex: 15
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A59 - U88 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 33

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 34
             LeftIndex: 16
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 16
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 19 20
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 18
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 18
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 18
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 18
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 18
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 18
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 18
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 18
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 18
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 18
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 18
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 18
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 18
pMakeMotifModelFromSSF:  16     Fixed Left  9 Right 18
pMakeMotifModelFromSSF:  17   Initial Left 10 Right 18
pMakeMotifModelFromSSF:  18     Fixed Left 10 Right 18
pMakeMotifModelFromSSF:  19   Initial Left 11 Right 18
pMakeMotifModelFromSSF:  20     Fixed Left 11 Right 18
pMakeMotifModelFromSSF:  21   Initial Left 12 Right 18
pMakeMotifModelFromSSF:  22     Fixed Left 12 Right 18
pMakeMotifModelFromSSF:  23   Initial Left 13 Right 18
pMakeMotifModelFromSSF:  24     Fixed Left 13 Right 18
pMakeMotifModelFromSSF:  25   Initial Left 14 Right 18
pMakeMotifModelFromSSF:  26     Fixed Left 14 Right 18
pMakeMotifModelFromSSF:  27   Initial Left 15 Right 18
pMakeMotifModelFromSSF:  28     Fixed Left 15 Right 18
pMakeMotifModelFromSSF:  29   Initial Left 15 Right 17
pMakeMotifModelFromSSF:  30     Fixed Left 15 Right 17
pMakeMotifModelFromSSF:  31   Initial Left 15 Right 16
pMakeMotifModelFromSSF:  32  Basepair Left 15 Right 16
pMakeMotifModelFromSSF:  33   Hairpin Left 16 Right 15
pNextNodeJunction: Found a hairpin at node 33
pNextNodeJunction: Found a hairpin at node 33

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_34739.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.3540
  -11.3540
  -11.3540

Timestamp 18-Jul-2025 22:47:37
pMakeSCFGModels: Making JAR3D model for motif group IL_34822.1, number 147 of 411
pMakeNodes starting loop:     a=3PDR|1|X|A|60 B=3PDR|1|X|U|81
  2 Basepair    60   81 AU cWW 
No need to probe because of interaction between a=3PDR|1|X|A|61 B=3PDR|1|X|A|80
  3 Basepair    61   80 AA tWH 
pMakeNodes probe for inserts:  a=3PDR|1|X|A|62 B=3PDR|1|X|A|79
    Insertion on left  3PDR|1|X|A|62
    Insertion on right 3PDR|1|X|A|79
pMakeNodesProbeForInsertions:  a 3PDR|1|X|A|63 interacts with 3PDR|1|X|C|78
pMakeNodesProbeForInsertions:  B 3PDR|1|X|C|78 interacts with 3PDR|1|X|A|63
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3PDR|1|X|C|78 interacts with 3PDR|1|X|A|63
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3PDR|1|X|A|63 B=3PDR|1|X|C|78
  4 Basepair    63   78 AC tHS 
No need to probe because of interaction between a=3PDR|1|X|A|64 B=3PDR|1|X|C|77
  5 Basepair    64   77 AC bif 
No need to probe because of interaction between a=3PDR|1|X|U|65 B=3PDR|1|X|G|76
  6 Basepair    65   76 UG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3PDR|1|X|A|62
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3PDR|1|X|A|79
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A60 - U81 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'AA'
               Comment: ' // Basepair A61 - A80 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3PDR|1|X|A|62'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3PDR|1|X|A|79'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A63 - C78 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A64 - C77 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U65 - G76 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_34822.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.4644
   -9.8297

Timestamp 18-Jul-2025 22:47:37
pMakeSCFGModels: Making JAR3D model for motif group IL_36516.3, number 148 of 411
pMakeNodes starting loop:     a=7EL1|1|B|A|42 B=7EL1|1|B|U|31
  2 Basepair    42   31 AU cWW 
No need to probe because of interaction between a=7EL1|1|B|A|43 B=7EL1|1|B|C|30
  3 Basepair    43   30 AC cWW 
pMakeNodes probe for inserts:  a=7EL1|1|B|U|44 B=7EL1|1|B|A|29
pMakeNodesProbeForInsertions:  a 7EL1|1|B|U|44 interacts with 7EL1|1|B|U|46
pMakeNodesProbeForInsertions:  B 7EL1|1|B|A|29 interacts with 7EL1|1|B|U|46
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 7EL1|1|B|A|29 interacts with 7EL1|1|B|U|46
pMakeNodes probed for insert:  a=7EL1|1|B|U|44 B=7EL1|1|B|A|29
pMakeNodes making a cluster near strand break a=7EL1|1|B|U|44 B=7EL1|1|B|A|29
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 5 and then 6 to 6
aa is 5 bb is 6
  4 Cluster   7EL1|1|B|U|44:7EL1|1|B|U|46 7EL1|1|B|A|29:7EL1|1|B|A|29
    LR Inter  7EL1|1|B|U|46 7EL1|1|B|A|29 cWW 
    LL Inter  7EL1|1|B|U|44 7EL1|1|B|U|46 cSH 
    Left  strand conserved insertion 7EL1|1|B|C|45 at position 2
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A42 - U31 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A43 - C30 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4 5]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UCU'
           RightLetter: 'A'
               Comment: ' // Cluster node 7EL1|1|B|U|44:7EL1|1|B|U|46 and 7EL1|1|B|A|29:7EL1|1|B|A|29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2551

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 6
pUpdateModelWithSSF: IL_36516.3 allow insertions from initial node 5?
ans =

    0.9923    0.0073    0.0004


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9923    0.0073    0.0004


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_36516.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4012
   -6.4012
   -6.9116
   -6.6599
   -6.8320
   -7.1720
   -6.2663

Timestamp 18-Jul-2025 22:47:38
pMakeSCFGModels: Making JAR3D model for motif group IL_36729.1, number 149 of 411
pMakeNodes starting loop:     a=8Z8U|1|B|G|6 B=8Z8U|1|B|C|36
  2 Basepair     6   36 GC cWW 
No need to probe because of interaction between a=8Z8U|1|B|A|7 B=8Z8U|1|B|A|35
  3 Basepair     7   35 AA cWW 
pMakeNodes probe for inserts:  a=8Z8U|1|B|G|8 B=8Z8U|1|B|G|34
    Insertion on left  8Z8U|1|B|G|8
    Insertion on left  8Z8U|1|B|C|9
    Insertion on left  8Z8U|1|B|C|10
    Insertion on right 8Z8U|1|B|G|34
    Insertion on right 8Z8U|1|B|A|33
    Insertion on right 8Z8U|1|B|U|32
    Insertion on right 8Z8U|1|B|C|31
    Insertion on right 8Z8U|1|B|G|30
pMakeNodesProbeForInsertions:  a 8Z8U|1|B|C|11 interacts with 8Z8U|1|B|G|29
pMakeNodesProbeForInsertions:  B 8Z8U|1|B|G|29 interacts with 8Z8U|1|B|C|11
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8Z8U|1|B|G|29 interacts with 8Z8U|1|B|C|14
pMakeNodes probed for insert:  a=8Z8U|1|B|C|11 B=8Z8U|1|B|G|29
pMakeNodes making a cluster near strand break a=8Z8U|1|B|C|11 B=8Z8U|1|B|G|29
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 6 to 9 and then 10 to 10
aa is 9 bb is 10
  4 Cluster   8Z8U|1|B|C|11:8Z8U|1|B|C|14 8Z8U|1|B|G|29:8Z8U|1|B|G|29
    LR Inter  8Z8U|1|B|C|11 8Z8U|1|B|G|29 tWH 
    LR Inter  8Z8U|1|B|C|14 8Z8U|1|B|G|29 cWW 
    LL Inter  8Z8U|1|B|C|11 8Z8U|1|B|A|13 cSH 
    Left  strand conserved insertion 8Z8U|1|B|A|12 at position 2
pMakeNodesCluster a=10 B=9 at the end
pMakeNodesCluster a=10 B=9 at the end
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4   Cluster Left  6  7  8  9 Right 10
pMakeMotifModelFromSSF:   5   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8Z8U|1|B|G|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8Z8U|1|B|C|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8Z8U|1|B|C|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8Z8U|1|B|G|34
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8Z8U|1|B|A|33
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8Z8U|1|B|U|32
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8Z8U|1|B|C|31
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8Z8U|1|B|G|30
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [17×17 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G6 - C36 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AGCC'
           RightLetter: 'GCUAGA'
               Comment: ' // Basepair A7 - A35 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8Z8U|1|B|G|8'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.0625

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8Z8U|1|B|C|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8Z8U|1|B|C|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8Z8U|1|B|G|34'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8Z8U|1|B|A|33'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8Z8U|1|B|U|32'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8Z8U|1|B|C|31'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8Z8U|1|B|G|30'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 21
             LeftIndex: [6 7 8 9]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CAAC'
           RightLetter: 'G'
               Comment: ' // Cluster node 8Z8U|1|B|C|11:8Z8U|1|B|C|14 and 8Z8U|1|B|G|29:8Z8U|1|B|G|29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.0625

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 15
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 15
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 15
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 15
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  12     Fixed Left  6 Right 14
pMakeMotifModelFromSSF:  13   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  14     Fixed Left  6 Right 13
pMakeMotifModelFromSSF:  15   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  16     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  17   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  18     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  19   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  20   Cluster Left  6  7  8  9 Right 10
pMakeMotifModelFromSSF:  21   Initial Left 10 Right  9
pMakeMotifModelFromSSF:  22   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 22
pUpdateModelWithSSF: IL_36729.1 allow insertions from initial node 21?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 22

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_36729.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.8345

Timestamp 18-Jul-2025 22:47:38
pMakeSCFGModels: Making JAR3D model for motif group IL_37015.1, number 150 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|97 B=5J7L|1|DA|G|85
pMakeNodes making a cluster near strand break a=5J7L|1|DA|C|97 B=5J7L|1|DA|G|85
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 6 and then 11 to 13
aa is 6 bb is 11
  2 Cluster   5J7L|1|DA|C|97:5J7L|1|DA|A|103 5J7L|1|DA|A|83:5J7L|1|DA|G|85
    LR Inter  5J7L|1|DA|A|103 5J7L|1|DA|A|83 tHS 
    LR Inter  5J7L|1|DA|G|98 5J7L|1|DA|A|84 tSS 
    LR Inter  5J7L|1|DA|A|101 5J7L|1|DA|A|84 tHH 
    LR Inter  5J7L|1|DA|C|97 5J7L|1|DA|G|85 cWW 
    LR Inter  5J7L|1|DA|A|103 5J7L|1|DA|G|85 tSS 
    LL Inter  5J7L|1|DA|C|97 5J7L|1|DA|A|103 cSS 
    Left  strand conserved insertion 5J7L|1|DA|U|99 at position 3
    Left  strand conserved insertion 5J7L|1|DA|U|100 at position 4
pMakeNodesCluster a=7 B=10 at the end
pMakeNodesCluster a=7 B=10 at the end
No need to probe because of interaction between a=5J7L|1|DA|A|104 B=5J7L|1|DA|U|82
  3 Basepair   104   82 AU tHS 
No need to probe because of interaction between a=5J7L|1|DA|C|105 B=5J7L|1|DA|G|81
  4 Basepair   105   81 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6 Right 11 12 13
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 0 0 0 0 0 1 1 1 1 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5 6]
            RightIndex: [11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CGUUAA'
           RightLetter: 'AAG'
               Comment: ' // Cluster node 5J7L|1|DA|C|97:5J7L|1|DA|A|103 and 5J7L|1|DA|A|83:5J7L|1|DA|G|85'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
          LeftNotInter: [3 4]
         RightNotInter: [1×0 double]
              NormCons: 0.0023
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A104 - U82 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C105 - G81 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6 Right 11 12 13
pMakeMotifModelFromSSF:   3   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   6   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_37015.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3531

Timestamp 18-Jul-2025 22:47:39
pMakeSCFGModels: Making JAR3D model for motif group IL_37603.1, number 151 of 411
pMakeNodes starting loop:     a=3SUX|1|X|C|89 B=3SUX|1|X|G|8||||17_555
  2 Basepair    89    8 CG cWW 
pMakeNodes probe for inserts:  a=3SUX|1|X|U|91 B=3SUX|1|X|A|7||||17_555
    Insertion on left  3SUX|1|X|U|91
    Insertion on left  3SUX|1|X|C|92
    Insertion on left  3SUX|1|X|U|93
    Insertion on left  3SUX|1|X|C|94
pMakeNodesProbeForInsertions:  a 3SUX|1|X|G|95 interacts with 3SUX|1|X|A|7||||17_555
pMakeNodesProbeForInsertions:  B 3SUX|1|X|A|7||||17_555 interacts with 3SUX|1|X|G|95
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3SUX|1|X|A|7||||17_555 interacts with 3SUX|1|X|G|95
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3SUX|1|X|G|95 B=3SUX|1|X|A|7||||17_555
  3 Basepair    95    7 GA cWW 
No need to probe because of interaction between a=3SUX|1|X|C|96 B=3SUX|1|X|G|6||||17_555
  4 Basepair    96    6 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3SUX|1|X|A|7||||17_555
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3SUX|1|X|G|8||||17_555
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3SUX|1|X|C|89
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3SUX|1|X|A|90
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CUCUC'
           RightLetter: 'G'
               Comment: ' // Basepair C89 - G8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3SUX|1|X|A|7||||17_555'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3SUX|1|X|G|8||||17_555'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3SUX|1|X|C|89'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3SUX|1|X|A|90'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G95 - A7 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C96 - G6 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  12  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  13   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_37603.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.6534

Timestamp 18-Jul-2025 22:47:39
pMakeSCFGModels: Making JAR3D model for motif group IL_37752.1, number 152 of 411
pMakeNodes starting loop:     a=8EPK|1|F|A2M|5 B=8EPK|1|F|UFT|26
  2 Basepair     5   26 AU cWW 
No need to probe because of interaction between a=8EPK|1|F|CFZ|6 B=8EPK|1|F|CFZ|25
  3 Basepair     6   25 CC bif 
No need to probe because of interaction between a=8EPK|1|F|UFT|7 B=8EPK|1|F|OMC|24
  4 Basepair     7   24 UC tSW 
pMakeNodes probe for inserts:  a=8EPK|1|F|A2M|8 B=8EPK|1|F|G|23
pMakeNodesProbeForInsertions:  a 8EPK|1|F|A2M|8 interacts with 8EPK|1|F|OMU|22
pMakeNodesProbeForInsertions:  B 8EPK|1|F|G|23 interacts with 8EPK|1|F|A2M|10
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8EPK|1|F|G|23 interacts with 8EPK|1|F|A2M|10
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8EPK|1|F|A2M|8 B=8EPK|1|F|G|23
pMakeNodes making a cluster near strand break a=8EPK|1|F|A2M|8 B=8EPK|1|F|G|23
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 8 to 9
aa is 5 bb is 8
  5 Cluster   8EPK|1|F|A2M|8:8EPK|1|F|A2M|10 8EPK|1|F|OMU|22:8EPK|1|F|G|23
    LR Inter  8EPK|1|F|A2M|8 8EPK|1|F|OMU|22 tHW 
    LR Inter  8EPK|1|F|A2M|10 8EPK|1|F|G|23 tHS 
pMakeNodesCluster a=6 B=7 at the end
pMakeNodesCluster a=6 B=7 at the end
No need to probe because of interaction between a=8EPK|1|F|OMG|13 B=8EPK|1|F|CFZ|21
  6 Basepair    13   21 GC cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right  8  9
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A5 - U26 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C6 - C25 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'C'
               Comment: ' // Basepair U7 - C24 tSW '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [4 5]
            RightIndex: [8 9]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AA'
           RightLetter: 'UG'
               Comment: ' // Cluster node 8EPK|1|F|A2M|8:8EPK|1|F|A2M|10 and 8EPK|1|F|OMU|22:8EPK|1|F|G|23'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2]
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G13 - C21 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right  8  9
pMakeMotifModelFromSSF:   6   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_37752.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.2318

Timestamp 18-Jul-2025 22:47:39
pMakeSCFGModels: Making JAR3D model for motif group IL_38186.6, number 153 of 411
pMakeNodes starting loop:     a=4LFB|1|A|C|569 B=4LFB|1|A|G|881
  2 Basepair   569  881 CG cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|G|570 B=4LFB|1|A|C|880
    Insertion on left  4LFB|1|A|G|570
    Insertion on left  4LFB|1|A|U|571
    Insertion on left  4LFB|1|A|A|573
    Insertion on left  4LFB|1|A|A|574
pMakeNodesProbeForInsertions:  a 4LFB|1|A|G|575 interacts with 4LFB|1|A|C|880
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|880 interacts with 4LFB|1|A|G|575
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|880 interacts with 4LFB|1|A|G|575
pMakeNodes probed for insert:  a=4LFB|1|A|G|575 B=4LFB|1|A|C|880
  3 Basepair   575  880 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|570
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|U|571
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|572
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|573
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGUAA'
           RightLetter: 'G'
               Comment: ' // Basepair C569 - G881 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|G|570'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|U|571'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|572'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|573'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G575 - C880 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  12   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_38186.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.1231
   -5.1231
   -5.1235
   -5.1235

Timestamp 18-Jul-2025 22:47:40
pMakeSCFGModels: Making JAR3D model for motif group IL_38394.1, number 154 of 411
pMakeNodes starting loop:     a=8F4O|1|B|C|38 B=8F4O|1|B|G|21
  2 Basepair    38   21 CG cWW 
pMakeNodes probe for inserts:  a=8F4O|1|B|U|39 B=8F4O|1|B|U|20
pMakeNodesProbeForInsertions:  a 8F4O|1|B|U|39 interacts with 8F4O|1|B|A|43
pMakeNodesProbeForInsertions:  B 8F4O|1|B|U|20 interacts with 8F4O|1|B|A|45
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8F4O|1|B|U|20 interacts with 8F4O|1|B|A|45
pMakeNodes probed for insert:  a=8F4O|1|B|U|39 B=8F4O|1|B|U|20
pMakeNodes making a cluster near strand break a=8F4O|1|B|U|39 B=8F4O|1|B|U|20
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 8 and then 9 to 9
aa is 8 bb is 9
  3 Cluster   8F4O|1|B|U|39:8F4O|1|B|A|45 8F4O|1|B|U|20:8F4O|1|B|U|20
    LR Inter  8F4O|1|B|A|45 8F4O|1|B|U|20 cWW 
    LL Inter  8F4O|1|B|U|39 8F4O|1|B|A|43 tWH 
    Left  strand conserved insertion 8F4O|1|B|G|40 at position 2
    Left  strand conserved insertion 8F4O|1|B|A|41 at position 3
    Left  strand conserved insertion 8F4O|1|B|G|42 at position 4
    Left  strand conserved insertion 8F4O|1|B|A|44 at position 6
pMakeNodesCluster a=9 B=8 at the end
pMakeNodesCluster a=9 B=8 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8 Right  9
pMakeMotifModelFromSSF:   4   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C38 - G21 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5 6 7 8]
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGAGAAA'
           RightLetter: 'U'
               Comment: ' // Cluster node 8F4O|1|B|U|39:8F4O|1|B|A|45 and 8F4O|1|B|U|20:8F4O|1|B|U|20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4 6]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  9 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_38394.1 allow insertions from initial node 4?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_38394.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.4278
   -5.4278

Timestamp 18-Jul-2025 22:47:40
pMakeSCFGModels: Making JAR3D model for motif group IL_38507.2, number 155 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|998 B=5J7L|1|DA|G|1157
  2 Basepair   998 1157 CG cWW 
No need to probe because of interaction between a=5J7L|1|DA|U|999 B=5J7L|1|DA|A|1155
  3 Basepair   999 1155 UA tWH 
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|1000 B=5J7L|1|DA|G|1154
    Insertion on left  5J7L|1|DA|A|1000
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|A|1001 interacts with 5J7L|1|DA|G|1154
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|1154 interacts with 5J7L|1|DA|A|1001
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|1154 interacts with 5J7L|1|DA|A|1001
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5J7L|1|DA|A|1001 B=5J7L|1|DA|G|1154
  4 Basepair  1001 1154 AG tHS 
No need to probe because of interaction between a=5J7L|1|DA|G|1002 B=5J7L|1|DA|C|1153
  5 Basepair  1002 1153 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|1000
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C998 - G1157 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: 'A'
               Comment: ' // Basepair U999 - A1155 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|1000'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1001 - G1154 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1002 - C1153 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_38507.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.0903
   -5.0903
   -5.0903
   -5.0903
   -7.5148
   -7.4926
   -7.4926
   -5.0903
   -8.5595
   -6.1120
   -5.0903
   -8.2090
   -7.3614
   -7.3614
   -6.4625
  -12.0779

Timestamp 18-Jul-2025 22:47:41
pMakeSCFGModels: Making JAR3D model for motif group IL_38634.5, number 156 of 411
pMakeNodes starting loop:     a=3K0J|1|E|U|59 B=3K0J|1|E|A|80
  2 Basepair    59   80 UA cWW 
No need to probe because of interaction between a=3K0J|1|E|G|60 B=3K0J|1|E|G|78
  3 Basepair    60   78 GG cWH 
No need to probe because of interaction between a=3K0J|1|E|A|61 B=3K0J|1|E|C|77
  4 Basepair    61   77 AC tWS 
No need to probe because of interaction between a=3K0J|1|E|C|63 B=3K0J|1|E|G|76
  5 Basepair    63   76 CG cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U59 - A80 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G60 - G78 cWH '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A61 - C77 tWS '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C63 - G76 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_38634.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.2389
   -7.2389

Timestamp 18-Jul-2025 22:47:41
pMakeSCFGModels: Making JAR3D model for motif group IL_38862.4, number 157 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|U|858 B=9DFE|1|1A|G|919
  2 Basepair   858  919 UG cWW 
No need to probe because of interaction between a=9DFE|1|1A|G|859 B=9DFE|1|1A|A|918
pMakeNodes making a cluster near strand break a=9DFE|1|1A|G|859 B=9DFE|1|1A|A|918
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 3 and then 8 to 9
aa is 3 bb is 8
  3 Cluster   9DFE|1|1A|G|859:9DFE|1|1A|U|860 9DFE|1|1A|A|917:9DFE|1|1A|A|918
    LR Inter  9DFE|1|1A|U|860 9DFE|1|1A|A|917 tWH 
    LR Inter  9DFE|1|1A|G|859 9DFE|1|1A|A|918 tSH 
    LL Inter  9DFE|1|1A|G|859 9DFE|1|1A|U|860 cSH 
pMakeNodesCluster a=4 B=7 at the end
pMakeNodesCluster a=4 B=7 at the end
No need to probe because of interaction between a=9DFE|1|1A|A|861 B=9DFE|1|1A|G|916
  4 Basepair   861  916 AG tHS 
No need to probe because of interaction between a=9DFE|1|1A|G|862 B=9DFE|1|1A|C|915
  5 Basepair   862  915 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  8  9
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U858 - G919 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3]
            RightIndex: [8 9]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'AA'
               Comment: ' // Cluster node 9DFE|1|1A|G|859:9DFE|1|1A|U|860 and 9DFE|1|1A|A|917:9DFE|1|1A|A|918'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0740

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A861 - G916 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G862 - C915 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  8  9
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_38862.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0319
   -6.0319
   -6.8336
   -7.0066
   -6.9371

Timestamp 18-Jul-2025 22:47:42
pMakeSCFGModels: Making JAR3D model for motif group IL_38969.1, number 158 of 411
pMakeNodes starting loop:     a=6N5P|1|A|C|36 B=6N5P|1|A|G|99
  2 Basepair    36   99 CG cWW 
pMakeNodes probe for inserts:  a=6N5P|1|A|G|37 B=6N5P|1|A|A|98
    Insertion on left  6N5P|1|A|G|37
    Insertion on left  6N5P|1|A|C|38
    Insertion on left  6N5P|1|A|U|39
    Insertion on left  6N5P|1|A|U|42
    Insertion on right 6N5P|1|A|A|98
pMakeNodesProbeForInsertions:  a 6N5P|1|A|G|44 interacts with 6N5P|1|A|C|97
pMakeNodesProbeForInsertions:  B 6N5P|1|A|C|97 interacts with 6N5P|1|A|G|44
pMakeNodesProbeForInsertions:  B 6N5P|1|A|C|97 interacts with 6N5P|1|A|G|44
pMakeNodes probed for insert:  a=6N5P|1|A|G|44 B=6N5P|1|A|C|97
  3 Basepair    44   97 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N5P|1|A|G|37
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N5P|1|A|C|38
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N5P|1|A|U|39
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N5P|1|A|U|40
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6N5P|1|A|U|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGCUU'
           RightLetter: 'AG'
               Comment: ' // Basepair C36 - G99 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6N5P|1|A|G|37'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6N5P|1|A|C|38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6N5P|1|A|U|39'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6N5P|1|A|U|40'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6N5P|1|A|U|43'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G44 - C97 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_38969.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3902

Timestamp 18-Jul-2025 22:47:42
pMakeSCFGModels: Making JAR3D model for motif group IL_41203.4, number 159 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|C|1004 B=9DFE|1|1A|G|1151
  2 Basepair  1004 1151 CG cWW 
pMakeNodes probe for inserts:  a=9DFE|1|1A|C|1005 B=9DFE|1|1A|C|1150
    Insertion on left  9DFE|1|1A|C|1005
    Insertion on left  9DFE|1|1A|C|1006
    Insertion on left  9DFE|1|1A|C|1007
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|C|1008 interacts with 9DFE|1|1A|A|1009
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|C|1150 interacts with 9DFE|1|1A|G|1011
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|C|1150 interacts with 9DFE|1|1A|G|1011
pMakeNodes probed for insert:  a=9DFE|1|1A|C|1008 B=9DFE|1|1A|C|1150
pMakeNodes making a cluster near strand break a=9DFE|1|1A|C|1008 B=9DFE|1|1A|C|1150
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 8 and then 9 to 9
aa is 8 bb is 9
  3 Cluster   9DFE|1|1A|C|1008:9DFE|1|1A|G|1011 9DFE|1|1A|C|1150:9DFE|1|1A|C|1150
    LR Inter  9DFE|1|1A|G|1011 9DFE|1|1A|C|1150 cWW 
    LL Inter  9DFE|1|1A|C|1008 9DFE|1|1A|A|1009 cSH 
    Left  strand conserved insertion 9DFE|1|1A|A|1010 at position 3
pMakeNodesCluster a=9 B=8 at the end
pMakeNodesCluster a=9 B=8 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  5  6  7  8 Right  9
pMakeMotifModelFromSSF:   4   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|C|1005
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|C|1006
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|C|1007
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CCCC'
           RightLetter: 'G'
               Comment: ' // Basepair C1004 - G1151 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|C|1005'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 3
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|C|1006'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|C|1007'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 10
             LeftIndex: [5 6 7 8]
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CAAG'
           RightLetter: 'C'
               Comment: ' // Cluster node 9DFE|1|1A|C|1008:9DFE|1|1A|G|1011 and 9DFE|1|1A|C|1150:9DFE|1|1A|C|1150'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 3
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   9   Cluster Left  5  6  7  8 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  9 Right  8
pMakeMotifModelFromSSF:  11   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 11
pUpdateModelWithSSF: IL_41203.4 allow insertions from initial node 10?
ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_41203.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8048
   -6.6751
   -6.8963
   -6.7204
   -6.7204
   -6.9423
   -6.9320
   -7.4948
   -8.5333
   -8.5333
   -7.2838

Timestamp 18-Jul-2025 22:47:43
pMakeSCFGModels: Making JAR3D model for motif group IL_41344.1, number 160 of 411
pMakeNodes starting loop:     a=4PDQ|1|A|G|16 B=4PDQ|1|B|C|32
  2 Basepair    16   32 GC cWW 
No need to probe because of interaction between a=4PDQ|1|A|A|17 B=4PDQ|1|B|A|31
  3 Basepair    17   31 AA tSH 
pMakeNodes probe for inserts:  a=4PDQ|1|A|A|18 B=4PDQ|1|B|C|30
    Insertion on left  4PDQ|1|A|A|18
pMakeNodesProbeForInsertions:  a 4PDQ|1|A|G|19 interacts with 4PDQ|1|B|C|30
pMakeNodesProbeForInsertions:  B 4PDQ|1|B|C|30 interacts with 4PDQ|1|A|G|19
pMakeNodesProbeForInsertions:  B 4PDQ|1|B|C|30 interacts with 4PDQ|1|A|G|19
pMakeNodes probed for insert:  a=4PDQ|1|A|G|19 B=4PDQ|1|B|C|30
  4 Basepair    19   30 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4PDQ|1|A|A|18
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G16 - C32 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'A'
               Comment: ' // Basepair A17 - A31 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4PDQ|1|A|A|18'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G19 - C30 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_41344.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.0024
   -7.3553

Timestamp 18-Jul-2025 22:47:43
pMakeSCFGModels: Making JAR3D model for motif group IL_41756.4, number 161 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|G|1111 B=8P9A|1|sR|C|1134
  2 Basepair  1111 1134 GC cWW 
No need to probe because of interaction between a=8P9A|1|sR|G|1112 B=8P9A|1|sR|A|1133
  3 Basepair  1112 1133 GA tSH 
No need to probe because of interaction between a=8P9A|1|sR|A|1113 B=8P9A|1|sR|A|1132
  4 Basepair  1113 1132 AA tHH 
pMakeNodes probe for inserts:  a=8P9A|1|sR|G|1114 B=8P9A|1|sR|A|1131
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|G|1114 interacts with 8P9A|1|sR|U|1115
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|A|1131 interacts with 8P9A|1|sR|U|1115
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|A|1131 interacts with 8P9A|1|sR|U|1115
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|sR|G|1114 B=8P9A|1|sR|A|1131
pMakeNodes making a cluster near strand break a=8P9A|1|sR|G|1114 B=8P9A|1|sR|A|1131
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 11 to 11
aa is 5 bb is 11
  5 Cluster   8P9A|1|sR|G|1114:8P9A|1|sR|U|1115 8P9A|1|sR|A|1131:8P9A|1|sR|A|1131
    LR Inter  8P9A|1|sR|U|1115 8P9A|1|sR|A|1131 tWH 
    LL Inter  8P9A|1|sR|G|1114 8P9A|1|sR|U|1115 cSH 
pMakeNodesCluster a=6 B=10 at the end
pMakeNodesCluster a=6 B=10 at the end
No need to probe because of interaction between a=8P9A|1|sR|A|1116 B=8P9A|1|sR|G|1130
  6 Basepair  1116 1130 AG tHS 
pMakeNodes probe for inserts:  a=8P9A|1|sR|U|1117 B=8P9A|1|sR|U|1129
    Insertion on left  8P9A|1|sR|U|1117
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|G|1118 interacts with 8P9A|1|sR|U|1129
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|1129 interacts with 8P9A|1|sR|G|1118
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|1129 interacts with 8P9A|1|sR|G|1118
pMakeNodes probed for insert:  a=8P9A|1|sR|G|1118 B=8P9A|1|sR|U|1129
  7 Basepair  1118 1129 GU cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 11
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   8   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|U|1117
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1111 - C1134 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1112 - A1133 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A1113 - A1132 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [4 5]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 8P9A|1|sR|G|1114:8P9A|1|sR|U|1115 and 8P9A|1|sR|A|1131:8P9A|1|sR|A|1131'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AU'
           RightLetter: 'G'
               Comment: ' // Basepair A1116 - G1130 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|U|1117'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1118 - U1129 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:   8     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:   9   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  10  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  11   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_41756.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8896
   -6.8896
   -6.8896
   -7.4789

Timestamp 18-Jul-2025 22:47:44
pMakeSCFGModels: Making JAR3D model for motif group IL_41853.1, number 162 of 411
pMakeNodes starting loop:     a=4V9F|1|0|C|1521 B=4V9F|1|0|G|1665
  2 Basepair  1521 1665 CG cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|1522 B=4V9F|1|0|A|1664
    Insertion on left  4V9F|1|0|A|1522
    Insertion on left  4V9F|1|0|G|1523
    Insertion on left  4V9F|1|0|U|1524
    Insertion on left  4V9F|1|0|G|1525
    Insertion on left  4V9F|1|0|A|1526
pMakeNodesProbeForInsertions:  a 4V9F|1|0|A|1527 interacts with 4V9F|1|0|A|1664
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|1664 interacts with 4V9F|1|0|A|1527
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|1664 interacts with 4V9F|1|0|A|1527
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4V9F|1|0|A|1527 B=4V9F|1|0|A|1664
  3 Basepair  1527 1664 AA tHH 
No need to probe because of interaction between a=4V9F|1|0|A|1528 B=4V9F|1|0|G|1663
  4 Basepair  1528 1663 AG tHS 
No need to probe because of interaction between a=4V9F|1|0|G|1529 B=4V9F|1|0|C|1662
  5 Basepair  1529 1662 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:   5  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   6   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|1522
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|G|1523
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|U|1524
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|G|1525
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|1526
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAGUGA'
           RightLetter: 'G'
               Comment: ' // Basepair C1521 - G1665 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|A|1522'
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|G|1523'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|U|1524'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|G|1525'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|A|1526'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A1527 - A1664 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1528 - G1663 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1529 - C1662 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 18
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 12
pMakeMotifModelFromSSF:  13  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:  14  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  15  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  16   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a hairpin at node 16

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_41853.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.1591

Timestamp 18-Jul-2025 22:47:44
pMakeSCFGModels: Making JAR3D model for motif group IL_42032.1, number 163 of 411
pMakeNodes starting loop:     a=4LFB|1|A|G|1175 B=4LFB|1|A|C|1161
pMakeNodes making a cluster near strand break a=4LFB|1|A|G|1175 B=4LFB|1|A|C|1161
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 9 to 11
aa is 2 bb is 9
  2 Cluster   4LFB|1|A|G|1175:4LFB|1|A|A|1176 4LFB|1|A|U|1159:4LFB|1|A|C|1161
    LR Inter  4LFB|1|A|A|1176 4LFB|1|A|G|1160 cWW 
    LR Inter  4LFB|1|A|G|1175 4LFB|1|A|C|1161 cWW 
    RR Inter  4LFB|1|A|U|1159 4LFB|1|A|C|1161 cSH 
pMakeNodesCluster a=3 B=8 at the end
pMakeNodesCluster a=3 B=8 at the end
pMakeNodes probe for inserts:  a=4LFB|1|A|G|1177 B=4LFB|1|A|C|1158
pMakeNodesProbeForInsertions:  a 4LFB|1|A|G|1177 interacts with 4LFB|1|A|G|1181
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|1158 interacts with 4LFB|1|A|G|1181
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|1158 interacts with 4LFB|1|A|G|1181
  3 Initial   1177 (0 insertion) and 1158 (0 insertion)
pMakeNodes probed for insert:  a=4LFB|1|A|G|1177 B=4LFB|1|A|C|1158
pMakeNodes making a cluster near strand break a=4LFB|1|A|G|1177 B=4LFB|1|A|C|1158
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 7 and then 8 to 8
aa is 7 bb is 8
  4 Cluster   4LFB|1|A|G|1177:4LFB|1|A|G|1181 4LFB|1|A|C|1158:4LFB|1|A|C|1158
    LR Inter  4LFB|1|A|G|1181 4LFB|1|A|C|1158 cWW 
    LL Inter  4LFB|1|A|G|1177 4LFB|1|A|G|1181 tWH 
    Left  strand conserved insertion 4LFB|1|A|G|1178 at position 2
    Left  strand conserved insertion 4LFB|1|A|A|1179 at position 3
    Left  strand conserved insertion 4LFB|1|A|A|1180 at position 4
pMakeNodesCluster a=8 B=7 at the end
pMakeNodesCluster a=8 B=7 at the end
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  9 10 11
pMakeMotifModelFromSSF:   3   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 0 1 1 1 1 1 1 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: [9 10 11]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GA'
           RightLetter: 'UGC'
               Comment: ' // Cluster node 4LFB|1|A|G|1175:4LFB|1|A|A|1176 and 4LFB|1|A|U|1159:4LFB|1|A|C|1161'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2510

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4LFB|1|A|G|1177 - 4LFB|1|A|C|1158 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4 5 6 7]
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGAAG'
           RightLetter: 'C'
               Comment: ' // Cluster node 4LFB|1|A|G|1177:4LFB|1|A|G|1181 and 4LFB|1|A|C|1158:4LFB|1|A|C|1158'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 0.2516

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  9 10 11
pMakeMotifModelFromSSF:   3   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6  7 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  8 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 6
pUpdateModelWithSSF: IL_42032.1 allow insertions from initial node 5?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_42032.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.7916
   -4.7916

Timestamp 18-Jul-2025 22:47:44
pMakeSCFGModels: Making JAR3D model for motif group IL_42218.2, number 164 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|1934 B=5J7L|1|DA|G|1964
  2 Basepair  1934 1964 CG cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|G|1935 B=5J7L|1|DA|5MC|1962
    Insertion on left  5J7L|1|DA|G|1935
    Insertion on right 5J7L|1|DA|5MC|1962
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|A|1936 interacts with 5J7L|1|DA|U|1943
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|1961 interacts with 5J7L|1|DA|G|1945
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|1961 interacts with 5J7L|1|DA|G|1945
pMakeNodes probed for insert:  a=5J7L|1|DA|A|1936 B=5J7L|1|DA|C|1961
pMakeNodes making a cluster near strand break a=5J7L|1|DA|A|1936 B=5J7L|1|DA|C|1961
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 10 and then 11 to 11
aa is 10 bb is 11
  3 Cluster   5J7L|1|DA|A|1936:5J7L|1|DA|G|1945 5J7L|1|DA|C|1961:5J7L|1|DA|C|1961
    LR Inter  5J7L|1|DA|G|1945 5J7L|1|DA|C|1961 cWW 
    LL Inter  5J7L|1|DA|U|1940 5J7L|1|DA|C|1941 cSH 
    LL Inter  5J7L|1|DA|U|1940 5J7L|1|DA|C|1942 tSW 
    LL Inter  5J7L|1|DA|A|1936 5J7L|1|DA|U|1943 cHW 
    Left  strand conserved insertion 5J7L|1|DA|A|1937 at position 2
    Left  strand conserved insertion 5J7L|1|DA|5MU|1939 at position 3
pMakeNodesCluster a=11 B=10 at the end
pMakeNodesCluster a=11 B=10 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  3  4  5  6  7  8  9 10 Right 11
pMakeMotifModelFromSSF:   4   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|1935
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|G|1945
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 0 0 0 0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CG'
           RightLetter: 'CG'
               Comment: ' // Basepair C1934 - G1964 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|1935'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.2549

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|G|1945'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [3 4 5 6 7 8 9 10]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAUUCCUG'
           RightLetter: 'C'
               Comment: ' // Cluster node 5J7L|1|DA|A|1936:5J7L|1|DA|G|1945 and 5J7L|1|DA|C|1961:5J7L|1|DA|C|1961'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.2549

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   7   Cluster Left  3  4  5  6  7  8  9 10 Right 11
pMakeMotifModelFromSSF:   8   Initial Left 11 Right 10
pMakeMotifModelFromSSF:   9   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 9
pUpdateModelWithSSF: IL_42218.2 allow insertions from initial node 8?
ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_42218.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.5114
   -8.5114
   -8.1750
   -9.5840
   -9.5840

Timestamp 18-Jul-2025 22:47:45
pMakeSCFGModels: Making JAR3D model for motif group IL_42231.1, number 165 of 411
pMakeNodes starting loop:     a=8CRE|1|1|U|3149 B=8CRE|1|1|A|3175
  2 Basepair  3149 3175 UA cWW 
pMakeNodes probe for inserts:  a=8CRE|1|1|C|3151 B=8CRE|1|1|G|3173
    Insertion on left  8CRE|1|1|C|3151
    Insertion on left  8CRE|1|1|G|3152
    Insertion on left  8CRE|1|1|A|3153
    Insertion on right 8CRE|1|1|G|3173
pMakeNodesProbeForInsertions:  a 8CRE|1|1|A|3154 interacts with 8CRE|1|1|A|3157
pMakeNodesProbeForInsertions:  B 8CRE|1|1|G|3170 interacts with 8CRE|1|1|A|3157
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8CRE|1|1|G|3170 interacts with 8CRE|1|1|A|3157
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8CRE|1|1|A|3154 B=8CRE|1|1|G|3170
pMakeNodes making a cluster near strand break a=8CRE|1|1|A|3154 B=8CRE|1|1|G|3170
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 7 and then 10 to 10
aa is 7 bb is 10
  3 Cluster   8CRE|1|1|A|3154:8CRE|1|1|A|3157 8CRE|1|1|G|3170:8CRE|1|1|G|3170
    LR Inter  8CRE|1|1|A|3157 8CRE|1|1|G|3170 cWW 
    LL Inter  8CRE|1|1|A|3154 8CRE|1|1|A|3157 cSS 
    Left  strand conserved insertion 8CRE|1|1|U|3155 at position 2
pMakeNodesCluster a=8 B=9 at the end
pMakeNodesCluster a=8 B=9 at the end
No need to probe because of interaction between a=8CRE|1|1|G|3158 B=8CRE|1|1|C|3169
  4 Basepair  3158 3169 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  5  6  7 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|A|3150
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|C|3151
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|G|3152
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|1|C|3169
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UCGA'
           RightLetter: 'GA'
               Comment: ' // Basepair U3149 - A3175 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|A|3150'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2407

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|C|3151'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|G|3152'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|1|C|3169'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 12
             LeftIndex: [5 6 7]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUA'
           RightLetter: 'G'
               Comment: ' // Cluster node 8CRE|1|1|A|3154:8CRE|1|1|A|3157 and 8CRE|1|1|G|3170:8CRE|1|1|G|3170'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2407

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G3158 - C3169 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  5 Right 10
pMakeMotifModelFromSSF:  11   Cluster Left  5  6  7 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  13  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  14   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_42231.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.7332
  -10.7332

Timestamp 18-Jul-2025 22:47:46
pMakeSCFGModels: Making JAR3D model for motif group IL_42314.1, number 166 of 411
pMakeNodes starting loop:     a=4KQY|1|A|U|52 B=4KQY|1|A|A|71
  2 Basepair    52   71 UA cWW 
No need to probe because of interaction between a=4KQY|1|A|G|53 B=4KQY|1|A|G|70
  3 Basepair    53   70 GG bif 
pMakeNodes probe for inserts:  a=4KQY|1|A|A|55 B=4KQY|1|A|U|69
    Insertion on left  4KQY|1|A|A|55
pMakeNodesProbeForInsertions:  a 4KQY|1|A|A|56 interacts with 4KQY|1|A|U|69
pMakeNodesProbeForInsertions:  B 4KQY|1|A|U|69 interacts with 4KQY|1|A|A|56
pMakeNodesProbeForInsertions:  B 4KQY|1|A|U|69 interacts with 4KQY|1|A|A|56
pMakeNodes probed for insert:  a=4KQY|1|A|A|56 B=4KQY|1|A|U|69
  4 Basepair    56   69 AU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KQY|1|A|U|54
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U52 - A71 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'G'
               Comment: ' // Basepair G53 - G70 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4KQY|1|A|U|54'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A56 - U69 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_42314.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7576

Timestamp 18-Jul-2025 22:47:46
pMakeSCFGModels: Making JAR3D model for motif group IL_42626.2, number 167 of 411
pMakeNodes starting loop:     a=4V9F|1|0|C|2547 B=4V9F|1|0|G|2609
  2 Basepair  2547 2609 CG cWW 
No need to probe because of interaction between a=4V9F|1|0|C|2548 B=4V9F|1|0|G|2606
  3 Basepair  2548 2606 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  2
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2547 - G2609 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2548 - G2606 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 3
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  2
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_42626.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0047
   -4.8482
   -8.3033
   -4.8482
   -8.3803
   -4.8482
   -5.5430
   -5.0163
   -5.0163
   -6.2754
   -6.1984
   -5.0137
   -5.0137
   -5.5456

Timestamp 18-Jul-2025 22:47:46
pMakeSCFGModels: Making JAR3D model for motif group IL_42771.1, number 168 of 411
pMakeNodes starting loop:     a=6JQ5|1|A|U|34 B=6JQ5|1|A|A|60
  2 Basepair    34   60 UA cWW 
No need to probe because of interaction between a=6JQ5|1|A|A|36 B=6JQ5|1|A|U|58
  3 Basepair    36   58 AU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  2
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U34 - A60 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A36 - U58 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 3
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  2
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_42771.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.8145
   -4.8145
   -4.8145
   -4.5634
   -4.6999
   -4.5079

Timestamp 18-Jul-2025 22:47:47
pMakeSCFGModels: Making JAR3D model for motif group IL_42778.1, number 169 of 411
pMakeNodes starting loop:     a=6QIT|1|A|C|2 B=6QIT|1|B|G|7
  2 Basepair     2    7 CG cWW 
pMakeNodes probe for inserts:  a=6QIT|1|A|A|3 B=6QIT|1|B|A|6
    Insertion on left  6QIT|1|A|A|3
    Insertion on left  6QIT|1|A|G|4
    Insertion on left  6QIT|1|A|C|5
    Insertion on left  6QIT|1|A|A|6
    Insertion on right 6QIT|1|B|A|6
    Insertion on right 6QIT|1|B|C|5
    Insertion on right 6QIT|1|B|G|4
pMakeNodesProbeForInsertions:  a 6QIT|1|A|G|7 interacts with 6QIT|1|B|C|2
pMakeNodesProbeForInsertions:  B 6QIT|1|B|C|2 interacts with 6QIT|1|A|G|7
pMakeNodesProbeForInsertions:  B 6QIT|1|B|C|2 interacts with 6QIT|1|A|G|7
pMakeNodes probed for insert:  a=6QIT|1|A|G|7 B=6QIT|1|B|C|2
  3 Basepair     7    2 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6QIT|1|A|A|3
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6QIT|1|A|G|4
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6QIT|1|A|C|5
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6QIT|1|A|A|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6QIT|1|B|C|5
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6QIT|1|B|G|4
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6QIT|1|B|A|3
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAGCA'
           RightLetter: 'GCAG'
               Comment: ' // Basepair C2 - G7 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6QIT|1|A|A|3'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6QIT|1|A|G|4'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6QIT|1|A|C|5'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6QIT|1|A|A|6'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6QIT|1|B|C|5'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6QIT|1|B|G|4'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6QIT|1|B|A|3'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G7 - C2 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 20
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  13     Fixed Left  6 Right  9
pMakeMotifModelFromSSF:  14   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  15     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  16   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  17  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  18   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a hairpin at node 18

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_42778.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.7794

Timestamp 18-Jul-2025 22:47:47
pMakeSCFGModels: Making JAR3D model for motif group IL_42997.3, number 170 of 411
pMakeNodes starting loop:     a=7VFT|1|A|C|8||||12_555 B=7VFT|1|A|G|16
  2 Basepair     8   16 CG cWW 
No need to probe because of interaction between a=7VFT|1|A|A|9||||12_555 B=7VFT|1|A|A|15
  3 Basepair     9   15 AA cWS 
No need to probe because of interaction between a=7VFT|1|A|G|10||||12_555 B=7VFT|1|A|C|14
  4 Basepair    10   14 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C8 - G16 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A9 - A15 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G10 - C14 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_42997.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.1240
   -5.7718
   -5.5426
   -5.1240
   -5.1240
   -5.5426
   -4.4671
   -5.1240
   -6.5627
   -6.5470
   -5.0415
   -5.0415
   -7.6892
   -5.0415
   -5.0415
   -5.0415
   -5.0415
   -5.2861
   -6.3422
   -5.9351

Timestamp 18-Jul-2025 22:47:48
pMakeSCFGModels: Making JAR3D model for motif group IL_43140.1, number 171 of 411
pMakeNodes starting loop:     a=7OAX|1|A|U|30 B=7OAX|1|A|G|17
  2 Basepair    30   17 UG cWW 
No need to probe because of interaction between a=7OAX|1|A|G|31 B=7OAX|1|A|C|16
pMakeNodes making a cluster near strand break a=7OAX|1|A|G|31 B=7OAX|1|A|C|16
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 7 and then 8 to 8
aa is 7 bb is 8
  3 Cluster   7OAX|1|A|G|31:7OAX|1|A|G|39 7OAX|1|A|C|16:7OAX|1|A|C|16
    LR Inter  7OAX|1|A|G|31 7OAX|1|A|C|16 tHH 
    LR Inter  7OAX|1|A|G|39 7OAX|1|A|C|16 cWW 
    LL Inter  7OAX|1|A|G|32 7OAX|1|A|G|37 cWH 
    Left  strand conserved insertion 7OAX|1|A|U|34 at position 3
    Left  strand conserved insertion 7OAX|1|A|G|36 at position 4
pMakeNodesCluster a=8 B=7 at the end
pMakeNodesCluster a=8 B=7 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U30 - G17 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5 6 7]
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGUGGG'
           RightLetter: 'C'
               Comment: ' // Cluster node 7OAX|1|A|G|31:7OAX|1|A|G|39 and 7OAX|1|A|C|16:7OAX|1|A|C|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [3 4]
         RightNotInter: [1×0 double]
              NormCons: 0.2489

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  8 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_43140.1 allow insertions from initial node 4?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_43140.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.2894

Timestamp 18-Jul-2025 22:47:48
pMakeSCFGModels: Making JAR3D model for motif group IL_43467.1, number 172 of 411
pMakeNodes starting loop:     a=1U6B|1|B|A|134 B=1U6B|1|B|U|173
  2 Basepair   134  173 AU cWW 
No need to probe because of interaction between a=1U6B|1|B|G|135 B=1U6B|1|B|G|170
  3 Basepair   135  170 GG tHW 
pMakeNodes probe for inserts:  a=1U6B|1|B|A|136 B=1U6B|1|B|G|169
    Insertion on left  1U6B|1|B|A|136
    Insertion on left  1U6B|1|B|C|137
    Insertion on left  1U6B|1|B|G|138
    Insertion on left  1U6B|1|B|G|139
    Insertion on left  1U6B|1|B|C|140
    Insertion on left  1U6B|1|B|A|141
    Insertion on left  1U6B|1|B|C|142
    Insertion on left  1U6B|1|B|C|143
    Insertion on right 1U6B|1|B|G|169
    Insertion on right 1U6B|1|B|A|168
    Insertion on right 1U6B|1|B|A|167
pMakeNodesProbeForInsertions:  a 1U6B|1|B|C|144 interacts with 1U6B|1|B|G|166
pMakeNodesProbeForInsertions:  B 1U6B|1|B|G|166 interacts with 1U6B|1|B|C|144
pMakeNodesProbeForInsertions:  B 1U6B|1|B|G|166 interacts with 1U6B|1|B|C|144
pMakeNodes probed for insert:  a=1U6B|1|B|C|144 B=1U6B|1|B|G|166
  4 Basepair   144  166 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:   5   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U6B|1|B|A|136
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U6B|1|B|C|137
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U6B|1|B|G|138
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U6B|1|B|G|139
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U6B|1|B|C|140
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U6B|1|B|A|141
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U6B|1|B|C|142
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1U6B|1|B|C|143
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1U6B|1|B|G|169
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1U6B|1|B|A|168
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1U6B|1|B|A|167
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [17×17 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A134 - U173 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GACGGCACC'
           RightLetter: 'AAGG'
               Comment: ' // Basepair G135 - G170 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U6B|1|B|A|136'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U6B|1|B|C|137'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U6B|1|B|G|138'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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      JunctionDeletion: []
          InterIndices: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U6B|1|B|G|139'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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          InterIndices: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U6B|1|B|C|140'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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          InterIndices: []
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                  rpar: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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          InterIndices: []
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                  rpar: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U6B|1|B|A|141'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U6B|1|B|C|142'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 10
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1U6B|1|B|C|143'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 11
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             LeftIndex: 11
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1U6B|1|B|G|169'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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                  rpar: []
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Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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                  lpar: []
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Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 23
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1U6B|1|B|A|168'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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                  Left: []
                 Right: []
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Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 25
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1U6B|1|B|A|167'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 26
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 27
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C144 - G166 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 29
             LeftIndex: 12
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 15
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 15
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 15
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 15
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 15
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 15
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 15
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 15
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 15
pMakeMotifModelFromSSF:  16     Fixed Left  9 Right 15
pMakeMotifModelFromSSF:  17   Initial Left 10 Right 15
pMakeMotifModelFromSSF:  18     Fixed Left 10 Right 15
pMakeMotifModelFromSSF:  19   Initial Left 11 Right 15
pMakeMotifModelFromSSF:  20     Fixed Left 11 Right 15
pMakeMotifModelFromSSF:  21   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  22     Fixed Left 11 Right 14
pMakeMotifModelFromSSF:  23   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  24     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  25   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  26  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  27   Hairpin Left 12 Right 11
pNextNodeJunction: Found a hairpin at node 27
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 1 of 1, pair 2,16 for nucleotide 2 (G) making self BPh with edge 1
pNextNodeJunction: Found a hairpin at node 27

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_43467.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.2918

Timestamp 18-Jul-2025 22:47:48
pMakeSCFGModels: Making JAR3D model for motif group IL_43547.1, number 173 of 411
pMakeNodes starting loop:     a=6UFG|1|A|C|53 B=6UFG|1|A|G|41
  2 Basepair    53   41 CG cWW 
No need to probe because of interaction between a=6UFG|1|A|C|54 B=6UFG|1|A|C|40
  3 Basepair    54   40 CC tSH 
No need to probe because of interaction between a=6UFG|1|A|A|55 B=6UFG|1|A|A|39
  4 Basepair    55   39 AA tHH 
pMakeNodes probe for inserts:  a=6UFG|1|A|G|56 B=6UFG|1|A|A|38
pMakeNodesProbeForInsertions:  a 6UFG|1|A|G|56 interacts with 6UFG|1|A|U|57
pMakeNodesProbeForInsertions:  B 6UFG|1|A|A|38 interacts with 6UFG|1|A|U|57
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 6UFG|1|A|A|38 interacts with 6UFG|1|A|U|57
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6UFG|1|A|G|56 B=6UFG|1|A|A|38
pMakeNodes making a cluster near strand break a=6UFG|1|A|G|56 B=6UFG|1|A|A|38
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 15 to 15
aa is 5 bb is 15
  5 Cluster   6UFG|1|A|G|56:6UFG|1|A|U|57 6UFG|1|A|A|38:6UFG|1|A|A|38
    LR Inter  6UFG|1|A|U|57 6UFG|1|A|A|38 tWH 
    LL Inter  6UFG|1|A|G|56 6UFG|1|A|U|57 cSH 
pMakeNodesCluster a=6 B=14 at the end
pMakeNodesCluster a=6 B=14 at the end
No need to probe because of interaction between a=6UFG|1|A|A|58 B=6UFG|1|A|G|37
  6 Basepair    58   37 AG tHS 
pMakeNodes probe for inserts:  a=6UFG|1|A|G|59 B=6UFG|1|A|A|36
    Insertion on left  6UFG|1|A|G|59
    Insertion on left  6UFG|1|A|A|60
    Insertion on right 6UFG|1|A|A|36
pMakeNodesProbeForInsertions:  a 6UFG|1|A|A|61 interacts with 6UFG|1|A|A|35
pMakeNodesProbeForInsertions:  B 6UFG|1|A|A|35 interacts with 6UFG|1|A|A|61
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6UFG|1|A|A|35 interacts with 6UFG|1|A|A|61
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6UFG|1|A|A|61 B=6UFG|1|A|A|35
  7 Basepair    61   35 AA cWW 
No need to probe because of interaction between a=6UFG|1|A|C|62 B=6UFG|1|A|G|34
  8 Basepair    62   34 CG cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 16
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 15
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right 14
pMakeMotifModelFromSSF:   7  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:   8  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   9   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|C|40
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6UFG|1|A|G|41
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6UFG|1|A|U|57
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C53 - G41 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C54 - C40 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A55 - A39 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [4 5]
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 6UFG|1|A|G|56:6UFG|1|A|U|57 and 6UFG|1|A|A|38:6UFG|1|A|A|38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AGA'
           RightLetter: 'AG'
               Comment: ' // Basepair A58 - G37 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|C|40'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6UFG|1|A|G|41'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 9
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6UFG|1|A|U|57'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A61 - A35 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C62 - G34 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 18
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 16
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 15
pMakeMotifModelFromSSF:   6   Initial Left  6 Right 14
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right 14
pMakeMotifModelFromSSF:   8     Fixed Left  7 Right 13
pMakeMotifModelFromSSF:   9   Initial Left  8 Right 13
pMakeMotifModelFromSSF:  10     Fixed Left  8 Right 13
pMakeMotifModelFromSSF:  11   Initial Left  9 Right 13
pMakeMotifModelFromSSF:  12     Fixed Left  9 Right 13
pMakeMotifModelFromSSF:  13   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  14  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  15  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  16   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a hairpin at node 16

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_43547.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2272
   -8.2272
   -8.4545

Timestamp 18-Jul-2025 22:47:49
pMakeSCFGModels: Making JAR3D model for motif group IL_43622.1, number 174 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|U|3373 B=8P9A|1|AR|A|3330
  2 Basepair  3373 3330 UA cWW 
No need to probe because of interaction between a=8P9A|1|AR|U|3374 B=8P9A|1|AR|U|3329
  3 Basepair  3374 3329 UU cWW 
pMakeNodes probe for inserts:  a=8P9A|1|AR|A|3375 B=8P9A|1|AR|G|3328
    Insertion on left  8P9A|1|AR|A|3375
    Insertion on left  8P9A|1|AR|A|3376
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|C|3378 interacts with 8P9A|1|AR|G|3328
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|G|3328 interacts with 8P9A|1|AR|C|3378
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|G|3328 interacts with 8P9A|1|AR|C|3378
pMakeNodes probed for insert:  a=8P9A|1|AR|C|3378 B=8P9A|1|AR|G|3328
  4 Basepair  3378 3328 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|A|3330
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|U|3373
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U3373 - A3330 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UAA'
           RightLetter: 'U'
               Comment: ' // Basepair U3374 - U3329 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|A|3330'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|U|3373'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C3378 - G3328 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_43622.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.3379
   -4.3379

Timestamp 18-Jul-2025 22:47:49
pMakeSCFGModels: Making JAR3D model for motif group IL_43644.1, number 175 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|A|2183 B=5J7L|1|DA|U|2106
  2 Basepair  2183 2106 AU cWW 
No need to probe because of interaction between a=5J7L|1|DA|A|2184 B=5J7L|1|DA|U|2105
  3 Basepair  2184 2105 AU tSH 
No need to probe because of interaction between a=5J7L|1|DA|U|2185 B=5J7L|1|DA|C|2104
  4 Basepair  2185 2104 UC cWW 
No need to probe because of interaction between a=5J7L|1|DA|G|2186 B=5J7L|1|DA|C|2103
  5 Basepair  2186 2103 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2183 - U2106 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2184 - U2105 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'C'
               Comment: ' // Basepair U2185 - C2104 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2186 - C2103 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_43644.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.6107
   -6.4109

Timestamp 18-Jul-2025 22:47:50
pMakeSCFGModels: Making JAR3D model for motif group IL_43858.1, number 176 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|U|553 B=8P9A|1|AR|G|538
  2 Basepair   553  538 UG cWW 
No need to probe because of interaction between a=8P9A|1|AR|A|554 B=8P9A|1|AR|A|537
  3 Basepair   554  537 AA tSH 
pMakeNodes probe for inserts:  a=8P9A|1|AR|U|555 B=8P9A|1|AR|U|536
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|U|555 interacts with 8P9A|1|AR|A|533
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|U|536 interacts with 8P9A|1|AR|A|557
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|U|536 interacts with 8P9A|1|AR|G|535
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|AR|U|555 B=8P9A|1|AR|U|536
pMakeNodes making a cluster near strand break a=8P9A|1|AR|U|555 B=8P9A|1|AR|U|536
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 6 and then 11 to 13
aa is 6 bb is 11
  4 Cluster   8P9A|1|AR|U|555:8P9A|1|AR|A|559 8P9A|1|AR|A|533:8P9A|1|AR|U|536
    LR Inter  8P9A|1|AR|U|555 8P9A|1|AR|A|533 tWH 
    LR Inter  8P9A|1|AR|A|559 8P9A|1|AR|A|533 cWW 
    LR Inter  8P9A|1|AR|A|557 8P9A|1|AR|U|536 cHW 
    LL Inter  8P9A|1|AR|U|555 8P9A|1|AR|U|556 cSH 
    LL Inter  8P9A|1|AR|U|556 8P9A|1|AR|A|559 cWH 
    RR Inter  8P9A|1|AR|G|535 8P9A|1|AR|U|536 cSH 
pMakeNodesCluster a=7 B=10 at the end
pMakeNodesCluster a=7 B=10 at the end
No need to probe because of interaction between a=8P9A|1|AR|G|560 B=8P9A|1|AR|A|532
  5 Basepair   560  532 GA cWW 
No need to probe because of interaction between a=8P9A|1|AR|C|561 B=8P9A|1|AR|G|531
  6 Basepair   561  531 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6 Right 11 12 13
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   7   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U553 - G538 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A554 - A537 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4 5 6]
            RightIndex: [11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUAA'
           RightLetter: 'AGU'
               Comment: ' // Cluster node 8P9A|1|AR|U|555:8P9A|1|AR|A|559 and 8P9A|1|AR|A|533:8P9A|1|AR|U|536'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0035

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G560 - A532 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C561 - G531 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6 Right 11 12 13
pMakeMotifModelFromSSF:   5   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   8   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_43858.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3681
   -8.0031

Timestamp 18-Jul-2025 22:47:50
pMakeSCFGModels: Making JAR3D model for motif group IL_44325.1, number 177 of 411
pMakeNodes starting loop:     a=5LYS|1|B|G|74 B=5LYS|1|B|C|35
  2 Basepair    74   35 GC cWW 
pMakeNodes probe for inserts:  a=5LYS|1|B|C|75 B=5LYS|1|B|C|33
pMakeNodesProbeForInsertions:  a 5LYS|1|B|C|75 interacts with 5LYS|1|B|G|78
pMakeNodesProbeForInsertions:  B 5LYS|1|B|C|33 interacts with 5LYS|1|B|G|78
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 5LYS|1|B|C|33 interacts with 5LYS|1|B|G|78
pMakeNodes probed for insert:  a=5LYS|1|B|C|75 B=5LYS|1|B|C|33
pMakeNodes making a cluster near strand break a=5LYS|1|B|C|75 B=5LYS|1|B|C|33
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 5 to 5
aa is 4 bb is 5
  3 Cluster   5LYS|1|B|C|75:5LYS|1|B|G|78 5LYS|1|B|C|33:5LYS|1|B|C|33
    LR Inter  5LYS|1|B|G|78 5LYS|1|B|C|33 cWW 
    LL Inter  5LYS|1|B|C|75 5LYS|1|B|G|78 cWH 
    Left  strand conserved insertion 5LYS|1|B|A|77 at position 2
pMakeNodesCluster a=5 B=4 at the end
pMakeNodesCluster a=5 B=4 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G74 - C35 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4]
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CAG'
           RightLetter: 'C'
               Comment: ' // Cluster node 5LYS|1|B|C|75:5LYS|1|B|G|78 and 5LYS|1|B|C|33:5LYS|1|B|C|33'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2500

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  5 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_44325.1 allow insertions from initial node 4?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_44325.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.8210

Timestamp 18-Jul-2025 22:47:51
pMakeSCFGModels: Making JAR3D model for motif group IL_44438.1, number 178 of 411
pMakeNodes starting loop:     a=8F4O|1|B|U|59 B=8F4O|1|B|A|80
  2 Basepair    59   80 UA cWW 
pMakeNodes probe for inserts:  a=8F4O|1|B|G|60 B=8F4O|1|B|U|79
    Insertion on left  8F4O|1|B|G|60
    Insertion on left  8F4O|1|B|A|61
    Insertion on left  8F4O|1|B|U|62
    Insertion on left  8F4O|1|B|C|63
    Insertion on right 8F4O|1|B|U|79
    Insertion on right 8F4O|1|B|G|78
    Insertion on right 8F4O|1|B|C|77
    Insertion on right 8F4O|1|B|G|76
pMakeNodesProbeForInsertions:  a 8F4O|1|B|U|64 interacts with 8F4O|1|B|A|75
pMakeNodesProbeForInsertions:  B 8F4O|1|B|A|75 interacts with 8F4O|1|B|U|64
pMakeNodesProbeForInsertions:  B 8F4O|1|B|A|75 interacts with 8F4O|1|B|U|64
pMakeNodes probed for insert:  a=8F4O|1|B|U|64 B=8F4O|1|B|A|75
  3 Basepair    64   75 UA cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8F4O|1|B|G|60
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8F4O|1|B|A|61
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8F4O|1|B|U|62
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8F4O|1|B|C|63
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8F4O|1|B|U|79
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8F4O|1|B|G|78
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8F4O|1|B|C|77
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8F4O|1|B|G|76
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGAUC'
           RightLetter: 'GCGUA'
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         Extensibility: []
                Delete: 0.0100
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                     Z: 1
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Node 3

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Node 4

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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           RightLetter: ''
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                Delete: []
              SubsProb: [5×5 double]
                     Z: []
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                     P: []
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Node 5

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 6

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           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
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         Extensibility: []
                Delete: []
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                     Z: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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                Delete: 1.0000e-03
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
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            LeftLetter: []
           RightLetter: []
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         Extensibility: []
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Node 9

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
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         Extensibility: []
                Delete: []
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                     Z: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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               Comment: ' // Fixed node on right for 8F4O|1|B|U|79'
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
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                     Z: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
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        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8F4O|1|B|G|78'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8F4O|1|B|C|77'
              NumLoops: []
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                Delete: 1.0000e-03
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                     Z: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 6
            RightIndex: 8
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        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8F4O|1|B|G|76'
              NumLoops: []
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         Extensibility: []
                Delete: 1.0000e-03
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                     Z: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
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         Extensibility: []
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                     Z: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U64 - A75 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 22
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  13     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  14   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  15     Fixed Left  6 Right  9
pMakeMotifModelFromSSF:  16   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  17     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  18   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  19  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  20   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Found a hairpin at node 20

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_44438.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.9246

Timestamp 18-Jul-2025 22:47:51
pMakeSCFGModels: Making JAR3D model for motif group IL_44465.1, number 179 of 411
pMakeNodes starting loop:     a=1SI2|1|B|U|403 B=1SI2|1|B|A|405||||4_675
  2 Basepair   403  405 UA cWW 
pMakeNodes probe for inserts:  a=1SI2|1|B|G|404 B=1SI2|1|B|G|404||||4_675
    Insertion on left  1SI2|1|B|G|404
    Insertion on right 1SI2|1|B|G|404||||4_675
pMakeNodesProbeForInsertions:  a 1SI2|1|B|A|405 interacts with 1SI2|1|B|U|403||||4_675
pMakeNodesProbeForInsertions:  B 1SI2|1|B|U|403||||4_675 interacts with 1SI2|1|B|A|405
pMakeNodesProbeForInsertions:  B 1SI2|1|B|U|403||||4_675 interacts with 1SI2|1|B|A|405
pMakeNodes probed for insert:  a=1SI2|1|B|A|405 B=1SI2|1|B|U|403||||4_675
  3 Basepair   405  403 AU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1SI2|1|B|G|404
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1SI2|1|B|G|404||||4_675
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
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        leftLengthDist: []
        leftLetterDist: []
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       rightLetterDist: []
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           RightLetter: ''
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                  Edge: [6×6 double]
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Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UG'
           RightLetter: 'GA'
               Comment: ' // Basepair U403 - A405 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
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               subtype: []
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                 Right: []
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                  rpar: [17×1 double]
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Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1SI2|1|B|G|404'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1SI2|1|B|G|404||||4_675'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A405 - U403 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   8   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_44465.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.9728
   -3.9728
   -4.2593
   -4.1976
   -4.5256
   -5.0594
   -4.5256
   -7.3112
   -7.9510

Timestamp 18-Jul-2025 22:47:51
pMakeSCFGModels: Making JAR3D model for motif group IL_44624.1, number 180 of 411
pMakeNodes starting loop:     a=7TZS|1|X|C|38 B=7TZS|1|X|G|21
  2 Basepair    38   21 CG cWW 
pMakeNodes probe for inserts:  a=7TZS|1|X|U|39 B=7TZS|1|X|U|20
pMakeNodesProbeForInsertions:  a 7TZS|1|X|U|39 interacts with 7TZS|1|X|A|43
pMakeNodesProbeForInsertions:  B 7TZS|1|X|U|20 interacts with 7TZS|1|X|A|45
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 7TZS|1|X|U|20 interacts with 7TZS|1|X|A|45
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=7TZS|1|X|U|39 B=7TZS|1|X|U|20
pMakeNodes making a cluster near strand break a=7TZS|1|X|U|39 B=7TZS|1|X|U|20
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 10 and then 11 to 13
aa is 10 bb is 11
  3 Cluster   7TZS|1|X|U|39:7TZS|1|X|C|48 7TZS|1|X|G|18:7TZS|1|X|U|20
    LR Inter  7TZS|1|X|C|48 7TZS|1|X|G|18 cWW 
    LR Inter  7TZS|1|X|G|42 7TZS|1|X|G|19 tSS 
    LR Inter  7TZS|1|X|A|47 7TZS|1|X|G|19 cWW 
    LR Inter  7TZS|1|X|A|45 7TZS|1|X|U|20 cWW 
    LL Inter  7TZS|1|X|U|39 7TZS|1|X|A|43 tWH 
    LL Inter  7TZS|1|X|A|41 7TZS|1|X|C|48 cSS 
    Left  strand conserved insertion 7TZS|1|X|G|40 at position 2
    Left  strand conserved insertion 7TZS|1|X|A|44 at position 6
pMakeNodesCluster a=11 B=10 at the end
pMakeNodesCluster a=11 B=10 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8  9 10 Right 11 12 13
pMakeMotifModelFromSSF:   4   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C38 - G21 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5 6 7 8 9 10]
            RightIndex: [11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGAGAAAAC'
           RightLetter: 'GGU'
               Comment: ' // Cluster node 7TZS|1|X|U|39:7TZS|1|X|C|48 and 7TZS|1|X|G|18:7TZS|1|X|U|20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8 9]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 6]
         RightNotInter: [1×0 double]
              NormCons: 0.0829

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8  9 10 Right 11 12 13
pMakeMotifModelFromSSF:   4   Initial Left 11 Right 10
pMakeMotifModelFromSSF:   5   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_44624.1 allow insertions from initial node 4?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_44624.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.0579
   -8.0579

Timestamp 18-Jul-2025 22:47:52
pMakeSCFGModels: Making JAR3D model for motif group IL_44874.1, number 181 of 411
pMakeNodes starting loop:     a=3NDB|1|M|C|192 B=3NDB|1|M|G|226
  2 Basepair   192  226 CG cWW 
No need to probe because of interaction between a=3NDB|1|M|G|193 B=3NDB|1|M|A|225
  3 Basepair   193  225 GA tSH 
No need to probe because of interaction between a=3NDB|1|M|A|194 B=3NDB|1|M|U|224
  4 Basepair   194  224 AU tHW 
pMakeNodes probe for inserts:  a=3NDB|1|M|A|195 B=3NDB|1|M|G|223
    Insertion on left  3NDB|1|M|A|195
    Insertion on left  3NDB|1|M|C|196
    Insertion on left  3NDB|1|M|C|197
pMakeNodesProbeForInsertions:  a 3NDB|1|M|C|198 interacts with 3NDB|1|M|G|223
pMakeNodesProbeForInsertions:  B 3NDB|1|M|G|223 interacts with 3NDB|1|M|C|198
pMakeNodesProbeForInsertions:  B 3NDB|1|M|G|223 interacts with 3NDB|1|M|C|198
pMakeNodes probed for insert:  a=3NDB|1|M|C|198 B=3NDB|1|M|G|223
  5 Basepair   198  223 CG cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NDB|1|M|A|195
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NDB|1|M|C|196
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NDB|1|M|C|197
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C192 - G226 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G193 - A225 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AACC'
           RightLetter: 'U'
               Comment: ' // Basepair A194 - U224 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NDB|1|M|A|195'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NDB|1|M|C|196'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NDB|1|M|C|197'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C198 - G223 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  6 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  12   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_44874.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4783

Timestamp 18-Jul-2025 22:47:52
pMakeSCFGModels: Making JAR3D model for motif group IL_45444.1, number 182 of 411
pMakeNodes starting loop:     a=1NUV|1|A|C|22 B=1NUV|1|B|G|46
  2 Basepair    22   46 CG cWW 
No need to probe because of interaction between a=1NUV|1|A|C|23 B=1NUV|1|B|A|45
  3 Basepair    23   45 CA bif 
pMakeNodes probe for inserts:  a=1NUV|1|A|G|24 B=1NUV|1|B|G|44
    Insertion on left  1NUV|1|A|G|24
    Insertion on left  1NUV|1|A|A|25
    Insertion on right 1NUV|1|B|G|44
pMakeNodesProbeForInsertions:  a 1NUV|1|A|C|27 interacts with 1NUV|1|B|G|43
pMakeNodesProbeForInsertions:  B 1NUV|1|B|G|43 interacts with 1NUV|1|A|C|27
pMakeNodesProbeForInsertions:  B 1NUV|1|B|G|43 interacts with 1NUV|1|A|C|27
pMakeNodes probed for insert:  a=1NUV|1|A|C|27 B=1NUV|1|B|G|43
  4 Basepair    27   43 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1NUV|1|A|G|24
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1NUV|1|A|A|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1NUV|1|B|G|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C22 - G46 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGA'
           RightLetter: 'GA'
               Comment: ' // Basepair C23 - A45 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1NUV|1|A|G|24'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1NUV|1|A|A|25'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1NUV|1|B|G|43'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C27 - G43 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_45444.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.2814
   -5.2814

Timestamp 18-Jul-2025 22:47:52
pMakeSCFGModels: Making JAR3D model for motif group IL_45896.1, number 183 of 411
pMakeNodes starting loop:     a=3IAB|1|R|C|64 B=3IAB|1|R|G|99
  2 Basepair    64   99 CG cWW 
pMakeNodes probe for inserts:  a=3IAB|1|R|A|65 B=3IAB|1|R|A|95
    Insertion on left  3IAB|1|R|A|65
    Insertion on left  3IAB|1|R|U|67
    Insertion on left  3IAB|1|R|A|68
    Insertion on left  3IAB|1|R|A|69
    Insertion on left  3IAB|1|R|A|71
    Insertion on right 3IAB|1|R|A|95
    Insertion on right 3IAB|1|R|A|93
pMakeNodesProbeForInsertions:  a 3IAB|1|R|G|73 interacts with 3IAB|1|R|C|88
pMakeNodesProbeForInsertions:  B 3IAB|1|R|C|88 interacts with 3IAB|1|R|G|73
pMakeNodesProbeForInsertions:  B 3IAB|1|R|C|88 interacts with 3IAB|1|R|G|73
pMakeNodes probed for insert:  a=3IAB|1|R|G|73 B=3IAB|1|R|C|88
  3 Basepair    73   88 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IAB|1|R|A|65
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IAB|1|R|G|66
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IAB|1|R|U|67
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IAB|1|R|A|68
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IAB|1|R|A|69
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3IAB|1|R|G|73
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3IAB|1|R|U|72
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAUAAA'
           RightLetter: 'AAG'
               Comment: ' // Basepair C64 - G99 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IAB|1|R|A|65'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IAB|1|R|G|66'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IAB|1|R|U|67'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IAB|1|R|A|68'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IAB|1|R|A|69'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3IAB|1|R|G|73'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3IAB|1|R|U|72'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G73 - C88 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 20
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  14   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  15     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  16   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  17  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  18   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a hairpin at node 18

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_45896.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -18.9206

Timestamp 18-Jul-2025 22:47:53
pMakeSCFGModels: Making JAR3D model for motif group IL_46086.1, number 184 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|C|1506 B=9DFE|1|1A|G|1482
  2 Basepair  1506 1482 CG cWW 
pMakeNodes probe for inserts:  a=9DFE|1|1A|A|1507 B=9DFE|1|1A|U|1481
    Insertion on left  9DFE|1|1A|A|1507
    Insertion on left  9DFE|1|1A|A|1508
    Insertion on left  9DFE|1|1A|A|1509|||A
    Insertion on left  9DFE|1|1A|A|1509|||B
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|G|1510 interacts with 9DFE|1|1A|U|1481
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|U|1481 interacts with 9DFE|1|1A|G|1510
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|U|1481 interacts with 9DFE|1|1A|G|1510
pMakeNodes probed for insert:  a=9DFE|1|1A|G|1510 B=9DFE|1|1A|U|1481
  3 Basepair  1510 1481 GU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|G|1482
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|C|1506
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|A|1507
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|A|1508
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAAAA'
           RightLetter: 'G'
               Comment: ' // Basepair C1506 - G1482 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|G|1482'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|C|1506'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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                  lpar: []
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|A|1507'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|A|1508'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1510 - U1481 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  12   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_46086.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7785

Timestamp 18-Jul-2025 22:47:53
pMakeSCFGModels: Making JAR3D model for motif group IL_46112.1, number 185 of 411
pMakeNodes starting loop:     a=4Y1M|1|B|A|44 B=4Y1M|1|B|U|64
  2 Basepair    44   64 AU cWW 
pMakeNodes probe for inserts:  a=4Y1M|1|B|A|45 B=4Y1M|1|B|G|63
    Insertion on left  4Y1M|1|B|A|45
    Insertion on left  4Y1M|1|B|C|46
    Insertion on left  4Y1M|1|B|U|49
    Insertion on left  4Y1M|1|B|U|50
    Insertion on left  4Y1M|1|B|U|51
pMakeNodesProbeForInsertions:  a 4Y1M|1|B|C|52 interacts with 4Y1M|1|B|G|63
pMakeNodesProbeForInsertions:  B 4Y1M|1|B|G|63 interacts with 4Y1M|1|B|C|52
pMakeNodesProbeForInsertions:  B 4Y1M|1|B|G|63 interacts with 4Y1M|1|B|C|52
pMakeNodes probed for insert:  a=4Y1M|1|B|C|52 B=4Y1M|1|B|G|63
  3 Basepair    52   63 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Y1M|1|B|A|45
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Y1M|1|B|C|46
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Y1M|1|B|A|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Y1M|1|B|U|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Y1M|1|B|U|49
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AACUUU'
           RightLetter: 'U'
               Comment: ' // Basepair A44 - U64 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4Y1M|1|B|A|45'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4Y1M|1|B|C|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                  lpar: []
                  rpar: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4Y1M|1|B|A|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4Y1M|1|B|U|48'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4Y1M|1|B|U|49'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                IBases: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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                  lpar: []
                  rpar: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C52 - G63 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  12   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  13  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  14   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_46112.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.6535

Timestamp 18-Jul-2025 22:47:53
pMakeSCFGModels: Making JAR3D model for motif group IL_46174.3, number 186 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|U|346 B=8CRE|1|CM|A|314
pMakeNodes making a cluster near strand break a=8CRE|1|CM|U|346 B=8CRE|1|CM|A|314
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 6 and then 9 to 12
aa is 6 bb is 9
  2 Cluster   8CRE|1|CM|U|346:8CRE|1|CM|C|352 8CRE|1|CM|A|310:8CRE|1|CM|A|314
    LR Inter  8CRE|1|CM|A|351 8CRE|1|CM|A|310 tHW 
    LR Inter  8CRE|1|CM|C|352 8CRE|1|CM|C|312 cWW 
    LR Inter  8CRE|1|CM|U|347 8CRE|1|CM|A|313 tSS 
    LR Inter  8CRE|1|CM|A|350 8CRE|1|CM|A|313 tSH 
    LR Inter  8CRE|1|CM|U|346 8CRE|1|CM|A|314 cWW 
    LR Inter  8CRE|1|CM|A|351 8CRE|1|CM|A|314 tSS 
    Left  strand conserved insertion 8CRE|1|CM|U|348 at position 3
pMakeNodesCluster a=7 B=8 at the end
pMakeNodesCluster a=7 B=8 at the end
No need to probe because of interaction between a=8CRE|1|CM|G|353 B=8CRE|1|CM|U|309
  3 Basepair   353  309 GU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6 Right  9 10 11 12
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 0 0 0 0 0 1 1 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5 6]
            RightIndex: [9 10 11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUUAAC'
           RightLetter: 'ACAA'
               Comment: ' // Cluster node 8CRE|1|CM|U|346:8CRE|1|CM|C|352 and 8CRE|1|CM|A|310:8CRE|1|CM|A|314'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
          LeftNotInter: 3
         RightNotInter: [1×0 double]
              NormCons: 0.0262
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G353 - U309 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6 Right  9 10 11 12
pMakeMotifModelFromSSF:   3   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_46174.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.8745
   -8.8745
  -10.2088
   -8.7917
  -13.8986

Timestamp 18-Jul-2025 22:47:54
pMakeSCFGModels: Making JAR3D model for motif group IL_46387.1, number 187 of 411
pMakeNodes starting loop:     a=2OEU|1|B|C|14 B=2OEU|1|A|G|5
  2 Basepair    14    5 CG cWW 
No need to probe because of interaction between a=2OEU|1|B|C|15 B=2OEU|1|A|U|4
  3 Basepair    15    4 CU cWW 
pMakeNodes probe for inserts:  a=2OEU|1|B|A|16 B=2OEU|1|A|A|3
    Insertion on left  2OEU|1|B|A|16
    Insertion on left  2OEU|1|B|A|17
pMakeNodesProbeForInsertions:  a 2OEU|1|B|U|18 interacts with 2OEU|1|A|A|3
pMakeNodesProbeForInsertions:  B 2OEU|1|A|A|3 interacts with 2OEU|1|B|U|18
pMakeNodesProbeForInsertions:  B 2OEU|1|A|A|3 interacts with 2OEU|1|B|U|18
pMakeNodes probed for insert:  a=2OEU|1|B|U|18 B=2OEU|1|A|A|3
  4 Basepair    18    3 UA cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2OEU|1|A|G|5
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2OEU|1|B|C|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C14 - G5 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAA'
           RightLetter: 'U'
               Comment: ' // Basepair C15 - U4 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2OEU|1|A|G|5'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2OEU|1|B|C|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U18 - A3 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_46387.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.6113
   -6.0473
   -7.8356

Timestamp 18-Jul-2025 22:47:54
pMakeSCFGModels: Making JAR3D model for motif group IL_47074.2, number 188 of 411
pMakeNodes starting loop:     a=4LFB|1|A|U|249 B=4LFB|1|A|G|275
  2 Basepair   249  275 UG cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|A|250 B=4LFB|1|A|A|274
    Insertion on left  4LFB|1|A|A|250
    Insertion on left  4LFB|1|A|G|251
pMakeNodesProbeForInsertions:  a 4LFB|1|A|U|252 interacts with 4LFB|1|A|A|274
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|274 interacts with 4LFB|1|A|U|252
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|274 interacts with 4LFB|1|A|U|252
pMakeNodes probed for insert:  a=4LFB|1|A|U|252 B=4LFB|1|A|A|274
  3 Basepair   252  274 UA cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|250
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|251
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UAG'
           RightLetter: 'G'
               Comment: ' // Basepair U249 - G275 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|250'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|G|251'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U252 - A274 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_47074.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.3677
   -3.3677
   -5.3934
   -7.3315

Timestamp 18-Jul-2025 22:47:55
pMakeSCFGModels: Making JAR3D model for motif group IL_47078.3, number 189 of 411
pMakeNodes starting loop:     a=5J7L|1|AA|U|1380 B=5J7L|1|AA|A|935
pMakeNodes making a cluster near strand break a=5J7L|1|AA|U|1380 B=5J7L|1|AA|A|935
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 4 and then 7 to 7
aa is 4 bb is 7
  2 Cluster   5J7L|1|AA|U|1380:5J7L|1|AA|C|1383 5J7L|1|AA|A|935:5J7L|1|AA|A|935
    LR Inter  5J7L|1|AA|U|1380 5J7L|1|AA|A|935 cWW 
    LR Inter  5J7L|1|AA|C|1383 5J7L|1|AA|A|935 cWS 
    Left  strand conserved insertion 5J7L|1|AA|U|1381 at position 2
    Left  strand conserved insertion 5J7L|1|AA|C|1382 at position 3
pMakeNodesCluster a=5 B=6 at the end
pMakeNodesCluster a=5 B=6 at the end
No need to probe because of interaction between a=5J7L|1|AA|C|1384 B=5J7L|1|AA|G|933
  3 Basepair  1384  933 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 0 0 0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4]
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUCC'
           RightLetter: 'A'
               Comment: ' // Cluster node 5J7L|1|AA|U|1380:5J7L|1|AA|C|1383 and 5J7L|1|AA|A|935:5J7L|1|AA|A|935'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.2458
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1384 - G933 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right  7
pMakeMotifModelFromSSF:   3   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_47078.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7240
   -5.7240
   -5.3866
   -5.3866

Timestamp 18-Jul-2025 22:47:55
pMakeSCFGModels: Making JAR3D model for motif group IL_47087.1, number 190 of 411
pMakeNodes starting loop:     a=3P59|1|E|G|51 B=3P59|1|F|C|112
  2 Basepair    51  112 GC cWW 
pMakeNodes probe for inserts:  a=3P59|1|E|G|52 B=3P59|1|F|C|111
    Insertion on left  3P59|1|E|G|52
    Insertion on left  3P59|1|E|A|53
    Insertion on left  3P59|1|E|A|54
pMakeNodesProbeForInsertions:  a 3P59|1|E|C|55 interacts with 3P59|1|F|G|110
pMakeNodesProbeForInsertions:  B 3P59|1|F|C|111 interacts with 3P59|1|E|A|57
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3P59|1|F|C|111 interacts with 3P59|1|E|A|57
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3P59|1|E|C|55 B=3P59|1|F|C|111
pMakeNodes making a cluster near strand break a=3P59|1|E|C|55 B=3P59|1|F|C|111
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 8 and then 9 to 10
aa is 8 bb is 9
  3 Cluster   3P59|1|E|C|55:3P59|1|E|C|58 3P59|1|F|G|110:3P59|1|F|C|111
    LR Inter  3P59|1|E|C|55 3P59|1|F|G|110 tWH 
    LR Inter  3P59|1|E|C|58 3P59|1|F|G|110 cWW 
    LR Inter  3P59|1|E|A|57 3P59|1|F|C|111 cWW 
    LL Inter  3P59|1|E|C|55 3P59|1|E|A|57 cSH 
    Left  strand conserved insertion 3P59|1|E|U|56 at position 2
pMakeNodesCluster a=9 B=8 at the end
pMakeNodesCluster a=9 B=8 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  5  6  7  8 Right  9 10
pMakeMotifModelFromSSF:   4   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3P59|1|E|G|52
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3P59|1|E|A|53
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3P59|1|E|A|54
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGAA'
           RightLetter: 'C'
               Comment: ' // Basepair G51 - C112 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3P59|1|E|G|52'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: [1 2]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.0149

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3P59|1|E|A|53'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3P59|1|E|A|54'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 10
             LeftIndex: [5 6 7 8]
            RightIndex: [9 10]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUAC'
           RightLetter: 'GC'
               Comment: ' // Cluster node 3P59|1|E|C|55:3P59|1|E|C|58 and 3P59|1|F|G|110:3P59|1|F|C|111'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: [1 2]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.0149

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9   Cluster Left  5  6  7  8 Right  9 10
pMakeMotifModelFromSSF:  10   Initial Left  9 Right  8
pMakeMotifModelFromSSF:  11   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 11
pUpdateModelWithSSF: IL_47087.1 allow insertions from initial node 10?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_47087.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0951

Timestamp 18-Jul-2025 22:47:55
pMakeSCFGModels: Making JAR3D model for motif group IL_47108.1, number 191 of 411
pMakeNodes starting loop:     a=5Y7M|1|D|U|39 B=5Y7M|1|D|A|11
  2 Basepair    39   11 UA cWW 
pMakeNodes probe for inserts:  a=5Y7M|1|D|G|40 B=5Y7M|1|D|U|9
    Insertion on left  5Y7M|1|D|G|40
    Insertion on left  5Y7M|1|D|A|41
    Insertion on left  5Y7M|1|D|A|42
pMakeNodesProbeForInsertions:  a 5Y7M|1|D|A|43 interacts with 5Y7M|1|D|U|9
pMakeNodesProbeForInsertions:  B 5Y7M|1|D|U|9 interacts with 5Y7M|1|D|A|43
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5Y7M|1|D|U|9 interacts with 5Y7M|1|D|A|43
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5Y7M|1|D|A|43 B=5Y7M|1|D|U|9
  3 Basepair    43    9 AU tHH 
No need to probe because of interaction between a=5Y7M|1|D|G|44 B=5Y7M|1|D|U|8
  4 Basepair    44    8 GU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5Y7M|1|D|U|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5Y7M|1|D|A|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5Y7M|1|D|A|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGAA'
           RightLetter: 'A'
               Comment: ' // Basepair U39 - A11 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5Y7M|1|D|U|9'
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5Y7M|1|D|A|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5Y7M|1|D|A|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A43 - U9 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G44 - U8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_47108.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.2610

Timestamp 18-Jul-2025 22:47:56
pMakeSCFGModels: Making JAR3D model for motif group IL_47346.2, number 192 of 411
pMakeNodes starting loop:     a=8CRE|1|1|C|1914 B=8CRE|1|1|G|1930
  2 Basepair  1914 1930 CG cWW 
No need to probe because of interaction between a=8CRE|1|1|G|1915 B=8CRE|1|1|A|1929
  3 Basepair  1915 1929 GA tSH 
No need to probe because of interaction between a=8CRE|1|1|U|1916 B=8CRE|1|1|A|1928
  4 Basepair  1916 1928 UA tSH 
No need to probe because of interaction between a=8CRE|1|1|A|1917 B=8CRE|1|1|A|1926
  5 Basepair  1917 1926 AA tHH 
No need to probe because of interaction between a=8CRE|1|1|A|1918 B=8CRE|1|1|G|1925
  6 Basepair  1918 1925 AG tHS 
No need to probe because of interaction between a=8CRE|1|1|C|1919 B=8CRE|1|1|G|1924
  7 Basepair  1919 1924 CG cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1914 - G1930 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1915 - A1929 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1916 - A1928 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A1917 - A1926 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1918 - G1925 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1919 - G1924 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_47346.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.9211
   -6.9211
   -6.5492
   -6.1326
   -6.6110
   -6.1326
   -6.1326

Timestamp 18-Jul-2025 22:47:56
pMakeSCFGModels: Making JAR3D model for motif group IL_47972.1, number 193 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|366 B=5J7L|1|DA|G|271
  2 Basepair   366  271 CG cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|G|367 B=5J7L|1|DA|A|270
    Insertion on left  5J7L|1|DA|G|367
    Insertion on left  5J7L|1|DA|A|368
    Insertion on left  5J7L|1|DA|U|369
    Insertion on right 5J7L|1|DA|A|270
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|G|370 interacts with 5J7L|1|DA|C|269
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|269 interacts with 5J7L|1|DA|G|370
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|269 interacts with 5J7L|1|DA|G|370
pMakeNodes probed for insert:  a=5J7L|1|DA|G|370 B=5J7L|1|DA|C|269
  3 Basepair   370  269 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|270
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|271
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|366
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|U|369
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGAU'
           RightLetter: 'AG'
               Comment: ' // Basepair C366 - G271 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|270'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|271'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|366'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|U|369'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G370 - C269 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_47972.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.3631

Timestamp 18-Jul-2025 22:47:57
pMakeSCFGModels: Making JAR3D model for motif group IL_48076.6, number 194 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|C|2496 B=9DFE|1|1A|G|2455
  2 Basepair  2496 2455 CG cWW 
pMakeNodes probe for inserts:  a=9DFE|1|1A|A|2497 B=9DFE|1|1A|G|2454
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|A|2497 interacts with 9DFE|1|1A|C|2498
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|G|2454 interacts with 9DFE|1|1A|C|2498
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|G|2454 interacts with 9DFE|1|1A|C|2498
pMakeNodes probed for insert:  a=9DFE|1|1A|A|2497 B=9DFE|1|1A|G|2454
pMakeNodes making a cluster near strand break a=9DFE|1|1A|A|2497 B=9DFE|1|1A|G|2454
pMakeNodesCluster: amax is 3 bmin is 4, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 3 and then 4 to 4
aa is 3 bb is 4
  3 Cluster   9DFE|1|1A|A|2497:9DFE|1|1A|C|2498 9DFE|1|1A|G|2454:9DFE|1|1A|G|2454
    LR Inter  9DFE|1|1A|C|2498 9DFE|1|1A|G|2454 cWW 
    LL Inter  9DFE|1|1A|A|2497 9DFE|1|1A|C|2498 cSH 
pMakeNodesCluster a=4 B=3 at the end
pMakeNodesCluster a=4 B=3 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2496 - G2455 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3]
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AC'
           RightLetter: 'G'
               Comment: ' // Cluster node 9DFE|1|1A|A|2497:9DFE|1|1A|C|2498 and 9DFE|1|1A|G|2454:9DFE|1|1A|G|2454'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2506

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  3
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_48076.6 allow insertions from initial node 4?
ans =

    0.9986    0.0013    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9986    0.0013    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_48076.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.3226
   -3.3226
   -3.8533
   -3.3226
   -3.3226
   -5.2846
   -4.5287
   -3.6770
   -4.0575
   -4.0575
   -4.1294
   -4.1765
   -4.7540
   -3.7031
   -3.6770
   -3.7031
   -3.7031
   -3.7031
   -5.1577
   -3.8221
   -4.7275
   -3.6770
   -4.7275
   -4.9460
   -3.3226
   -4.7540
   -4.7275
   -4.5555
   -4.5555
   -3.7750
   -3.7750
   -3.7750
   -5.3241
   -7.8468
   -5.3241
   -4.4794
   -3.7263
   -7.5238
   -3.7263
   -6.9071
   -8.5110

Timestamp 18-Jul-2025 22:47:58
pMakeSCFGModels: Making JAR3D model for motif group IL_48444.6, number 195 of 411
pMakeNodes starting loop:     a=1L9A|1|B|U|117 B=1L9A|1|B|A|234
  2 Basepair   117  234 UA cWW 
pMakeNodes probe for inserts:  a=1L9A|1|B|A|118 B=1L9A|1|B|G|232
    Insertion on left  1L9A|1|B|A|118
    Insertion on right 1L9A|1|B|G|232
pMakeNodesProbeForInsertions:  a 1L9A|1|B|A|119 interacts with 1L9A|1|B|A|231
pMakeNodesProbeForInsertions:  B 1L9A|1|B|A|231 interacts with 1L9A|1|B|A|119
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 1L9A|1|B|A|231 interacts with 1L9A|1|B|A|119
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=1L9A|1|B|A|119 B=1L9A|1|B|A|231
  3 Basepair   119  231 AA cWW 
No need to probe because of interaction between a=1L9A|1|B|G|120 B=1L9A|1|B|C|230
  4 Basepair   120  230 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1L9A|1|B|A|118
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1L9A|1|B|G|232
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: 'GA'
               Comment: ' // Basepair U117 - A234 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1L9A|1|B|A|118'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1L9A|1|B|G|232'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A119 - A231 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G120 - C230 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_48444.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8168
   -7.8168
  -11.8582
   -9.8020

Timestamp 18-Jul-2025 22:47:58
pMakeSCFGModels: Making JAR3D model for motif group IL_49061.1, number 196 of 411
pMakeNodes starting loop:     a=4LFB|1|A|C|1440 B=4LFB|1|A|G|1461
  2 Basepair  1440 1461 CG cWW 
No need to probe because of interaction between a=4LFB|1|A|G|1441 B=4LFB|1|A|A|1460
  3 Basepair  1441 1460 GA tSH 
pMakeNodes probe for inserts:  a=4LFB|1|A|G|1442 B=4LFB|1|A|C|1459
    Insertion on left  4LFB|1|A|G|1442
    Insertion on left  4LFB|1|A|A|1446
pMakeNodesProbeForInsertions:  a 4LFB|1|A|G|1447 interacts with 4LFB|1|A|C|1459
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|1459 interacts with 4LFB|1|A|G|1447
pMakeNodesProbeForInsertions:  B 4LFB|1|A|C|1459 interacts with 4LFB|1|A|G|1447
pMakeNodes probed for insert:  a=4LFB|1|A|G|1447 B=4LFB|1|A|C|1459
  4 Basepair  1447 1459 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|1442
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|1443
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1440 - G1461 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGA'
           RightLetter: 'A'
               Comment: ' // Basepair G1441 - A1460 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|G|1442'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|G|1443'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1447 - C1459 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_49061.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.6778
   -8.8115
   -7.2469
   -7.6615
   -8.3503
  -14.3321

Timestamp 18-Jul-2025 22:47:59
pMakeSCFGModels: Making JAR3D model for motif group IL_49612.1, number 197 of 411
pMakeNodes starting loop:     a=5J7L|1|AA|C|1051 B=5J7L|1|AA|2MG|1207
  2 Basepair  1051 1207 CG cWW 
pMakeNodes probe for inserts:  a=5J7L|1|AA|G|1052 B=5J7L|1|AA|G|1206
    Insertion on left  5J7L|1|AA|G|1052
    Insertion on left  5J7L|1|AA|G|1053
pMakeNodesProbeForInsertions:  a 5J7L|1|AA|C|1054 interacts with 5J7L|1|AA|G|1206
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|G|1206 interacts with 5J7L|1|AA|C|1054
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|G|1206 interacts with 5J7L|1|AA|C|1054
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5J7L|1|AA|C|1054 B=5J7L|1|AA|G|1206
  3 Basepair  1054 1206 CG tHS 
pMakeNodes probe for inserts:  a=5J7L|1|AA|A|1055 B=5J7L|1|AA|U|1205
    Insertion on left  5J7L|1|AA|A|1055
    Insertion on right 5J7L|1|AA|U|1205
pMakeNodesProbeForInsertions:  a 5J7L|1|AA|U|1056 interacts with 5J7L|1|AA|A|1204
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|A|1204 interacts with 5J7L|1|AA|U|1056
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|A|1204 interacts with 5J7L|1|AA|U|1056
pMakeNodes probed for insert:  a=5J7L|1|AA|U|1056 B=5J7L|1|AA|A|1204
  4 Basepair  1056 1204 UA cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|G|1052
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|G|1053
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|A|1055
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|AA|U|1205
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGG'
           RightLetter: 'G'
               Comment: ' // Basepair C1051 - G1207 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|G|1052'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|G|1053'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: 'UG'
               Comment: ' // Basepair C1054 - G1206 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|A|1055'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|AA|U|1205'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1056 - A1204 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  11   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  13   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_49612.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.7763
  -10.8661

Timestamp 18-Jul-2025 22:47:59
pMakeSCFGModels: Making JAR3D model for motif group IL_49714.1, number 198 of 411
pMakeNodes starting loop:     a=3TZR|1|A|G|52 B=3TZR|1|B|C|111
pMakeNodes making a cluster near strand break a=3TZR|1|A|G|52 B=3TZR|1|B|C|111
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 4 and then 7 to 7
aa is 4 bb is 7
  2 Cluster   3TZR|1|A|G|52:3TZR|1|A|A|57 3TZR|1|B|C|111:3TZR|1|B|C|111
    LR Inter  3TZR|1|A|G|52 3TZR|1|B|C|111 cWW 
    LR Inter  3TZR|1|A|A|57 3TZR|1|B|C|111 cWS 
    Left  strand conserved insertion 3TZR|1|A|C|55 at position 2
    Left  strand conserved insertion 3TZR|1|A|U|56 at position 3
pMakeNodesCluster a=5 B=6 at the end
pMakeNodesCluster a=5 B=6 at the end
No need to probe because of interaction between a=3TZR|1|A|C|58 B=3TZR|1|B|G|110
  3 Basepair    58  110 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4]
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCUA'
           RightLetter: 'C'
               Comment: ' // Cluster node 3TZR|1|A|G|52:3TZR|1|A|A|57 and 3TZR|1|B|C|111:3TZR|1|B|C|111'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.2498
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C58 - G110 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right  7
pMakeMotifModelFromSSF:   3   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_49714.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.5706

Timestamp 18-Jul-2025 22:47:59
pMakeSCFGModels: Making JAR3D model for motif group IL_49751.4, number 199 of 411
pMakeNodes starting loop:     a=8VMA|1|C|C|51 B=8VMA|1|C|G|75
  2 Basepair    51   75 CG cWW 
No need to probe because of interaction between a=8VMA|1|C|U|52 B=8VMA|1|C|U|74
  3 Basepair    52   74 UU cWW 
No need to probe because of interaction between a=8VMA|1|C|C|53 B=8VMA|1|C|U|73
  4 Basepair    53   73 CU cWW 
No need to probe because of interaction between a=8VMA|1|C|C|54 B=8VMA|1|C|C|72
  5 Basepair    54   72 CC cWW 
No need to probe because of interaction between a=8VMA|1|C|U|55 B=8VMA|1|C|A|71
  6 Basepair    55   71 UA cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C51 - G75 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U52 - U74 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'U'
               Comment: ' // Basepair C53 - U73 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C54 - C72 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U55 - A71 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_49751.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.1049
   -8.1049
   -7.3230
   -7.2614
   -7.2614
   -7.3230
   -8.7767
   -8.9331
  -10.7372
  -10.6441
  -12.2580
  -10.6962
  -10.9074
  -10.9609
  -14.2215
  -13.7697

Timestamp 18-Jul-2025 22:48:00
pMakeSCFGModels: Making JAR3D model for motif group IL_49767.8, number 200 of 411
pMakeNodes starting loop:     a=7A0S|1|X|G|2717 B=7A0S|1|X|C|2747
  2 Basepair  2717 2747 GC cWW 
No need to probe because of interaction between a=7A0S|1|X|A|2718 B=7A0S|1|X|G|2746
  3 Basepair  2718 2746 AG cWW 
No need to probe because of interaction between a=7A0S|1|X|U|2719 B=7A0S|1|X|A|2744
  4 Basepair  2719 2744 UA tWH 
pMakeNodes probe for inserts:  a=7A0S|1|X|A|2720 B=7A0S|1|X|G|2743
    Insertion on left  7A0S|1|X|A|2720
pMakeNodesProbeForInsertions:  a 7A0S|1|X|A|2721 interacts with 7A0S|1|X|G|2743
pMakeNodesProbeForInsertions:  B 7A0S|1|X|G|2743 interacts with 7A0S|1|X|A|2721
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 7A0S|1|X|G|2743 interacts with 7A0S|1|X|A|2721
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=7A0S|1|X|A|2721 B=7A0S|1|X|G|2743
  5 Basepair  2721 2743 AG tHS 
No need to probe because of interaction between a=7A0S|1|X|C|2722 B=7A0S|1|X|G|2742
  6 Basepair  2722 2742 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7A0S|1|X|A|2720
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2717 - C2747 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A2718 - G2746 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: 'A'
               Comment: ' // Basepair U2719 - A2744 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7A0S|1|X|A|2720'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A2721 - G2743 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2722 - G2742 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_49767.8_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7495
   -6.7495
   -6.8423
   -7.5303
   -7.5054
  -10.5700

Timestamp 18-Jul-2025 22:48:01
pMakeSCFGModels: Making JAR3D model for motif group IL_49867.1, number 201 of 411
pMakeNodes starting loop:     a=1YLS|1|B|C|228 B=1YLS|1|B|G|217
  2 Basepair   228  217 CG cWW 
No need to probe because of interaction between a=1YLS|1|B|A|229 B=1YLS|1|B|G|216
  3 Basepair   229  216 AG cWW 
No need to probe because of interaction between a=1YLS|1|B|A|230 B=1YLS|1|B|C|215
  4 Basepair   230  215 AC bif 
No need to probe because of interaction between a=1YLS|1|B|U|231 B=1YLS|1|B|C|214
  5 Basepair   231  214 UC tSH 
pMakeNodes probe for inserts:  a=1YLS|1|B|A|232 B=1YLS|1|B|G|213
    Insertion on right 1YLS|1|B|G|213
pMakeNodesProbeForInsertions:  a 1YLS|1|B|A|232 interacts with 1YLS|1|B|U|212
pMakeNodesProbeForInsertions:  B 1YLS|1|B|U|212 interacts with 1YLS|1|B|A|232
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 1YLS|1|B|U|212 interacts with 1YLS|1|B|A|232
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=1YLS|1|B|A|232 B=1YLS|1|B|U|212
  6 Basepair   232  212 AU tHW 
pMakeNodes probe for inserts:  a=1YLS|1|B|C|233 B=1YLS|1|B|G|211
    Insertion on left  1YLS|1|B|C|233
    Insertion on left  1YLS|1|B|U|234
pMakeNodesProbeForInsertions:  a 1YLS|1|B|C|235 interacts with 1YLS|1|B|G|211
pMakeNodesProbeForInsertions:  B 1YLS|1|B|G|211 interacts with 1YLS|1|B|C|235
pMakeNodesProbeForInsertions:  B 1YLS|1|B|G|211 interacts with 1YLS|1|B|C|235
pMakeNodes probed for insert:  a=1YLS|1|B|C|235 B=1YLS|1|B|G|211
  7 Basepair   235  211 CG cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 12
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   8   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1YLS|1|B|U|231
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1YLS|1|B|G|216
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1YLS|1|B|G|217
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C228 - G217 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A229 - G216 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A230 - C215 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'GC'
               Comment: ' // Basepair U231 - C214 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1YLS|1|B|U|231'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'ACU'
           RightLetter: 'U'
               Comment: ' // Basepair A232 - U212 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1YLS|1|B|G|216'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1YLS|1|B|G|217'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C235 - G211 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 12
pMakeMotifModelFromSSF:   6     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  6 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  11     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  12   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  13  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  14   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_49867.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.3205

Timestamp 18-Jul-2025 22:48:01
pMakeSCFGModels: Making JAR3D model for motif group IL_49971.1, number 202 of 411
pMakeNodes starting loop:     a=1NTA|1|A|C|5 B=1NTA|1|B|G|115
  2 Basepair     5  115 CG cWW 
pMakeNodes probe for inserts:  a=1NTA|1|A|G|6 B=1NTA|1|B|G|114
pMakeNodesProbeForInsertions:  a 1NTA|1|A|G|6 interacts with 1NTA|1|A|G|13
pMakeNodesProbeForInsertions:  B 1NTA|1|B|G|114 interacts with 1NTA|1|A|C|7
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 1NTA|1|B|G|114 interacts with 1NTA|1|A|C|7
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=1NTA|1|A|G|6 B=1NTA|1|B|G|114
pMakeNodes making a cluster near strand break a=1NTA|1|A|G|6 B=1NTA|1|B|G|114
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 7 and then 8 to 9
aa is 7 bb is 8
  3 Cluster   1NTA|1|A|G|6:1NTA|1|A|G|13 1NTA|1|B|C|113:1NTA|1|B|G|114
    LR Inter  1NTA|1|A|G|13 1NTA|1|B|C|113 cWW 
    LR Inter  1NTA|1|A|C|7 1NTA|1|B|G|114 cWW 
    LL Inter  1NTA|1|A|G|6 1NTA|1|A|G|13 cWH 
    Left  strand conserved insertion 1NTA|1|A|A|8 at position 3
    Left  strand conserved insertion 1NTA|1|A|U|11 at position 4
    Left  strand conserved insertion 1NTA|1|A|G|12 at position 5
pMakeNodesCluster a=8 B=7 at the end
pMakeNodesCluster a=8 B=7 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7 Right  8  9
pMakeMotifModelFromSSF:   4   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C5 - G115 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5 6 7]
            RightIndex: [8 9]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCAUGG'
           RightLetter: 'CG'
               Comment: ' // Cluster node 1NTA|1|A|G|6:1NTA|1|A|G|13 and 1NTA|1|B|C|113:1NTA|1|B|G|114'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: [1 2]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [3 4 5]
         RightNotInter: [1×0 double]
              NormCons: 0.2515

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7 Right  8  9
pMakeMotifModelFromSSF:   4   Initial Left  8 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_49971.1 allow insertions from initial node 4?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_49971.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.8516

Timestamp 18-Jul-2025 22:48:01
pMakeSCFGModels: Making JAR3D model for motif group IL_50694.7, number 203 of 411
pMakeNodes starting loop:     a=4LFB|1|A|U|751 B=4LFB|1|A|A|655
  2 Basepair   751  655 UA cWW 
No need to probe because of interaction between a=4LFB|1|A|G|752 B=4LFB|1|A|G|654
pMakeNodes making a cluster near strand break a=4LFB|1|A|G|752 B=4LFB|1|A|G|654
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 5 to 5
aa is 4 bb is 5
  3 Cluster   4LFB|1|A|G|752:4LFB|1|A|C|754 4LFB|1|A|G|654:4LFB|1|A|G|654
    LR Inter  4LFB|1|A|G|752 4LFB|1|A|G|654 tSH 
    LR Inter  4LFB|1|A|C|754 4LFB|1|A|G|654 cWW 
    Left  strand conserved insertion 4LFB|1|A|A|753 at position 2
pMakeNodesCluster a=5 B=4 at the end
pMakeNodesCluster a=5 B=4 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U751 - A655 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4]
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAC'
           RightLetter: 'G'
               Comment: ' // Cluster node 4LFB|1|A|G|752:4LFB|1|A|C|754 and 4LFB|1|A|G|654:4LFB|1|A|G|654'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2516

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  5 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_50694.7 allow insertions from initial node 4?
ans =

    0.9980    0.0019    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9980    0.0019    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_50694.7_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.6490
   -3.6490
   -3.6490
   -3.6490
   -3.6490
   -4.0897
   -3.4958
   -4.0897
   -5.4704
   -3.5673
   -3.5673
   -4.3093
   -4.0897
   -4.0897
   -3.5673
   -4.0897
   -4.0897
   -4.7343
   -4.1875
   -4.0897
   -4.3093
   -4.3093
   -4.3093
   -6.3240
   -6.1267
   -5.7183
   -5.7183

Timestamp 18-Jul-2025 22:48:02
pMakeSCFGModels: Making JAR3D model for motif group IL_50715.3, number 204 of 411
pMakeNodes starting loop:     a=4WF9|1|X|C|1168 B=4WF9|1|X|G|1074
  2 Basepair  1168 1074 CG cWW 
No need to probe because of interaction between a=4WF9|1|X|G|1169 B=4WF9|1|X|A|1073
  3 Basepair  1169 1073 GA tSH 
No need to probe because of interaction between a=4WF9|1|X|A|1170 B=4WF9|1|X|A|1072
  4 Basepair  1170 1072 AA tHH 
pMakeNodes probe for inserts:  a=4WF9|1|X|A|1172 B=4WF9|1|X|A|1071
    Insertion on left  4WF9|1|X|A|1172
    Insertion on left  4WF9|1|X|A|1173
    Insertion on right 4WF9|1|X|A|1071
    Insertion on right 4WF9|1|X|A|1070
pMakeNodesProbeForInsertions:  a 4WF9|1|X|G|1175 interacts with 4WF9|1|X|U|1176
pMakeNodesProbeForInsertions:  B 4WF9|1|X|G|1069 interacts with 4WF9|1|X|G|1183
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4WF9|1|X|G|1069 interacts with 4WF9|1|X|G|1183
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4WF9|1|X|G|1175 B=4WF9|1|X|G|1069
pMakeNodes making a cluster near strand break a=4WF9|1|X|G|1175 B=4WF9|1|X|G|1069
pMakeNodesCluster: amax is 14 bmin is 15, use_amax is 1
pMakeNodesCluster: Cluster goes from 6 to 13 and then 16 to 16
aa is 13 bb is 16
  5 Cluster   4WF9|1|X|G|1175:4WF9|1|X|G|1183 4WF9|1|X|G|1069:4WF9|1|X|G|1069
    LR Inter  4WF9|1|X|G|1183 4WF9|1|X|G|1069 tWW 
    LL Inter  4WF9|1|X|G|1175 4WF9|1|X|U|1176 cSH 
    LL Inter  4WF9|1|X|C|1179 4WF9|1|X|G|1182 tWH 
    Left  strand conserved insertion 4WF9|1|X|A|1177 at position 3
    Left  strand conserved insertion 4WF9|1|X|G|1180 at position 5
    Left  strand conserved insertion 4WF9|1|X|G|1181 at position 6
pMakeNodesCluster a=14 B=15 at the end
pMakeNodesCluster a=14 B=15 at the end
No need to probe because of interaction between a=4WF9|1|X|C|1184 B=4WF9|1|X|G|1068
  6 Basepair  1184 1068 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 21
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 21
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 20
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 19
pMakeMotifModelFromSSF:   5   Cluster Left  6  7  8  9 10 11 12 13 Right 16
pMakeMotifModelFromSSF:   6  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:   7   Hairpin Left 15 Right 14
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|A|1071
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|A|1072
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WF9|1|X|C|1178
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WF9|1|X|A|1177
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 21
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [21×21 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1168 - G1074 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1169 - A1073 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAA'
           RightLetter: 'AAA'
               Comment: ' // Basepair A1170 - A1072 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|A|1071'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [3 5 6]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|A|1072'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 15
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WF9|1|X|C|1178'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WF9|1|X|A|1177'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 14
             LeftIndex: [6 7 8 9 10 11 12 13]
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUACGGGG'
           RightLetter: 'G'
               Comment: ' // Cluster node 4WF9|1|X|G|1175:4WF9|1|X|G|1183 and 4WF9|1|X|G|1069:4WF9|1|X|G|1069'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: 1
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [3 5 6]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 14
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 14
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1184 - G1068 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 18
             LeftIndex: 15
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 15
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 21
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 21
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 20
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 19
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 18
pMakeMotifModelFromSSF:   6   Initial Left  5 Right 18
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right 18
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 18
pMakeMotifModelFromSSF:   9     Fixed Left  6 Right 18
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 17
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 17
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 16
pMakeMotifModelFromSSF:  13   Cluster Left  6  7  8  9 10 11 12 13 Right 16
pMakeMotifModelFromSSF:  14   Initial Left 14 Right 15
pMakeMotifModelFromSSF:  15  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:  16   Hairpin Left 15 Right 14
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a hairpin at node 16

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_50715.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -16.8843
  -17.8317
  -15.7279
  -14.8806

Timestamp 18-Jul-2025 22:48:03
pMakeSCFGModels: Making JAR3D model for motif group IL_50730.2, number 205 of 411
pMakeNodes starting loop:     a=8CRE|1|1|U|1641 B=8CRE|1|1|A|1806
  2 Basepair  1641 1806 UA cWW 
No need to probe because of interaction between a=8CRE|1|1|G|1642 B=8CRE|1|1|A|1805
  3 Basepair  1642 1805 GA tSH 
No need to probe because of interaction between a=8CRE|1|1|A|1643 B=8CRE|1|1|G|1804
  4 Basepair  1643 1804 AG tHS 
No need to probe because of interaction between a=8CRE|1|1|A|1644 B=8CRE|1|1|G|1803
  5 Basepair  1644 1803 AG tHS 
No need to probe because of interaction between a=8CRE|1|1|U|1645 B=8CRE|1|1|A|1802
  6 Basepair  1645 1802 UA cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1641 - A1806 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1642 - A1805 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1643 - G1804 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1644 - G1803 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1645 - A1802 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_50730.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.6772
   -6.6772
   -8.6957
   -6.3745
   -6.3745
   -6.4891
   -6.3745
   -6.3745
   -8.7065
   -6.4385
   -7.3632
   -8.7065
   -6.3745
   -6.5411
   -6.5411
   -9.3110
   -6.8320
   -6.8457
   -6.5729

Timestamp 18-Jul-2025 22:48:04
pMakeSCFGModels: Making JAR3D model for motif group IL_51191.1, number 206 of 411
pMakeNodes starting loop:     a=6OL3|1|C|C|122 B=6OL3|1|C|G|37
  2 Basepair   122   37 CG cWW 
pMakeNodes probe for inserts:  a=6OL3|1|C|A|123 B=6OL3|1|C|A|36
    Insertion on left  6OL3|1|C|A|123
    Insertion on left  6OL3|1|C|G|124
    Insertion on left  6OL3|1|C|G|125
    Insertion on left  6OL3|1|C|U|126
    Insertion on right 6OL3|1|C|A|36
pMakeNodesProbeForInsertions:  a 6OL3|1|C|U|128 interacts with 6OL3|1|C|A|35
pMakeNodesProbeForInsertions:  B 6OL3|1|C|A|35 interacts with 6OL3|1|C|U|128
pMakeNodesProbeForInsertions:  B 6OL3|1|C|A|35 interacts with 6OL3|1|C|U|128
pMakeNodes probed for insert:  a=6OL3|1|C|U|128 B=6OL3|1|C|A|35
  3 Basepair   128   35 UA cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6OL3|1|C|A|36
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6OL3|1|C|G|37
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6OL3|1|C|C|122
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6OL3|1|C|A|123
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6OL3|1|C|U|126
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAGGU'
           RightLetter: 'AG'
               Comment: ' // Basepair C122 - G37 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6OL3|1|C|A|36'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6OL3|1|C|G|37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6OL3|1|C|C|122'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6OL3|1|C|A|123'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6OL3|1|C|U|126'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U128 - A35 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_51191.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.9316

Timestamp 18-Jul-2025 22:48:04
pMakeSCFGModels: Making JAR3D model for motif group IL_51265.3, number 207 of 411
pMakeNodes starting loop:     a=3SIV|1|C|C|33 B=3SIV|1|F|G|50
  2 Basepair    33   50 CG cWW 
No need to probe because of interaction between a=3SIV|1|C|A|34 B=3SIV|1|F|A|49
pMakeNodes making a cluster near strand break a=3SIV|1|C|A|34 B=3SIV|1|F|A|49
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 9 to 9
aa is 4 bb is 9
  3 Cluster   3SIV|1|C|A|34:3SIV|1|C|G|37 3SIV|1|F|A|49:3SIV|1|F|A|49
    LR Inter  3SIV|1|C|A|34 3SIV|1|F|A|49 tSS 
    LR Inter  3SIV|1|C|G|37 3SIV|1|F|A|49 tSH 
    Left  strand conserved insertion 3SIV|1|C|A|35 at position 2
pMakeNodesCluster a=5 B=8 at the end
pMakeNodesCluster a=5 B=8 at the end
No need to probe because of interaction between a=3SIV|1|C|A|38 B=3SIV|1|F|G|48
  4 Basepair    38   48 AG tHS 
No need to probe because of interaction between a=3SIV|1|C|G|39 B=3SIV|1|F|U|47
  5 Basepair    39   47 GU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C33 - G50 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4]
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAG'
           RightLetter: 'A'
               Comment: ' // Cluster node 3SIV|1|C|A|34:3SIV|1|C|G|37 and 3SIV|1|F|A|49:3SIV|1|F|A|49'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2278

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A38 - G48 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G39 - U47 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_51265.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.5912
   -4.5912
   -4.5912
   -5.6956
   -4.8730
   -4.8730

Timestamp 18-Jul-2025 22:48:05
pMakeSCFGModels: Making JAR3D model for motif group IL_51387.2, number 208 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|G|738 B=9DFE|1|1A|C|758
  2 Basepair   738  758 GC cWW 
pMakeNodes probe for inserts:  a=9DFE|1|1A|G|739 B=9DFE|1|1A|U|757
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|G|739 interacts with 9DFE|1|1A|U|740
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|U|757 interacts with 9DFE|1|1A|U|740
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|U|757 interacts with 9DFE|1|1A|U|740
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=9DFE|1|1A|G|739 B=9DFE|1|1A|U|757
pMakeNodes making a cluster near strand break a=9DFE|1|1A|G|739 B=9DFE|1|1A|U|757
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 3 and then 6 to 6
aa is 3 bb is 6
  3 Cluster   9DFE|1|1A|G|739:9DFE|1|1A|U|740 9DFE|1|1A|U|757:9DFE|1|1A|U|757
    LR Inter  9DFE|1|1A|U|740 9DFE|1|1A|U|757 cWW 
    LL Inter  9DFE|1|1A|G|739 9DFE|1|1A|U|740 cSH 
pMakeNodesCluster a=4 B=5 at the end
pMakeNodesCluster a=4 B=5 at the end
No need to probe because of interaction between a=9DFE|1|1A|G|741 B=9DFE|1|1A|C|756
  4 Basepair   741  756 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G738 - C758 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'U'
               Comment: ' // Cluster node 9DFE|1|1A|G|739:9DFE|1|1A|U|740 and 9DFE|1|1A|U|757:9DFE|1|1A|U|757'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.3031

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G741 - C756 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_51387.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.9486
   -4.9623
   -4.9486
   -4.9623
   -5.3277
   -6.7656
   -6.7656
   -6.3665
   -6.3665
   -8.4809
   -8.4809
   -6.3665
   -8.1753
   -6.3665
   -5.9035
   -5.9035
   -5.9035
   -6.2761
   -7.1053
   -9.3801

Timestamp 18-Jul-2025 22:48:06
pMakeSCFGModels: Making JAR3D model for motif group IL_51454.3, number 209 of 411
pMakeNodes starting loop:     a=6DLR|1|A|C|39 B=6DLR|1|A|G|22
pMakeNodes making a cluster near strand break a=6DLR|1|A|C|39 B=6DLR|1|A|G|22
pMakeNodesCluster: amax is 3 bmin is 4, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 5 to 5
aa is 2 bb is 5
  2 Cluster   6DLR|1|A|C|39:6DLR|1|A|U|40 6DLR|1|A|G|22:6DLR|1|A|G|22
    LR Inter  6DLR|1|A|C|39 6DLR|1|A|G|22 cWW 
    LR Inter  6DLR|1|A|U|40 6DLR|1|A|G|22 tHS 
    LL Inter  6DLR|1|A|C|39 6DLR|1|A|U|40 cSH 
pMakeNodesCluster a=3 B=4 at the end
pMakeNodesCluster a=3 B=4 at the end
No need to probe because of interaction between a=6DLR|1|A|G|41 B=6DLR|1|A|C|21
  3 Basepair    41   21 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CU'
           RightLetter: 'G'
               Comment: ' // Cluster node 6DLR|1|A|C|39:6DLR|1|A|U|40 and 6DLR|1|A|G|22:6DLR|1|A|G|22'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0162
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G41 - C21 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  5
pMakeMotifModelFromSSF:   3   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_51454.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.9595
   -5.0790
   -3.9595
   -3.9595
   -5.0790
   -8.3891
   -2.7505
   -4.4829
   -2.7505
   -2.7505
   -3.9595
   -2.7505
   -2.7505
   -5.0163
   -2.7382
   -3.0257
   -3.9595
   -5.3232
   -5.4450
   -5.3232
   -4.6187
   -2.7382
   -2.7382
   -5.8823
   -2.7382
   -3.0286
   -5.2648
   -4.9091
   -2.7505
   -4.4829
   -4.6187
   -4.6187
   -2.7505
   -3.0286
   -4.6187
   -2.7382
   -5.7970
   -4.6187
   -4.6187
   -5.2678
   -3.0286
   -5.8823
   -3.0286
   -4.6630
   -2.7382

Timestamp 18-Jul-2025 22:48:07
pMakeSCFGModels: Making JAR3D model for motif group IL_51479.1, number 210 of 411
pMakeNodes starting loop:     a=2OE8|1|A|C|1407 B=2OE8|1|B|G|1494
  2 Basepair  1407 1494 CG cWW 
pMakeNodes probe for inserts:  a=2OE8|1|A|G|1408 B=2OE8|1|B|A|1492
    Insertion on left  2OE8|1|A|G|1408
pMakeNodesProbeForInsertions:  a 2OE8|1|A|C|1409 interacts with 2OE8|1|B|A|1492
pMakeNodesProbeForInsertions:  B 2OE8|1|B|A|1492 interacts with 2OE8|1|A|C|1409
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 2OE8|1|B|A|1492 interacts with 2OE8|1|A|C|1409
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=2OE8|1|A|C|1409 B=2OE8|1|B|A|1492
  3 Basepair  1409 1492 CA cWS 
No need to probe because of interaction between a=2OE8|1|A|U|1410 B=2OE8|1|B|A|1490
  4 Basepair  1410 1490 UA cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2OE8|1|A|G|1408
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CG'
           RightLetter: 'G'
               Comment: ' // Basepair C1407 - G1494 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2OE8|1|A|G|1408'
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C1409 - A1492 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1410 - A1490 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_51479.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.9950
   -6.9950
   -6.9950
   -6.9950
   -8.3757
   -8.5467
  -10.2887
   -9.6056
   -8.5467
  -10.0943

Timestamp 18-Jul-2025 22:48:07
pMakeSCFGModels: Making JAR3D model for motif group IL_52743.1, number 211 of 411
pMakeNodes starting loop:     a=5NWQ|1|A|G|29 B=5NWQ|1|A|C|20
pMakeNodes making a cluster near strand break a=5NWQ|1|A|G|29 B=5NWQ|1|A|C|20
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 4 and then 10 to 10
aa is 4 bb is 10
  2 Cluster   5NWQ|1|A|G|29:5NWQ|1|A|A|32 5NWQ|1|A|C|20:5NWQ|1|A|C|20
    LR Inter  5NWQ|1|A|G|29 5NWQ|1|A|C|20 cWW 
    LL Inter  5NWQ|1|A|G|29 5NWQ|1|A|A|32 tSW 
    Left  strand conserved insertion 5NWQ|1|A|A|30 at position 2
    Left  strand conserved insertion 5NWQ|1|A|C|31 at position 3
pMakeNodesCluster a=5 B=9 at the end
pMakeNodesCluster a=5 B=9 at the end
pMakeNodes probe for inserts:  a=5NWQ|1|A|A|33 B=5NWQ|1|A|A|19
    Insertion on left  5NWQ|1|A|A|33
pMakeNodesProbeForInsertions:  a 5NWQ|1|A|G|34 interacts with 5NWQ|1|A|A|19
pMakeNodesProbeForInsertions:  B 5NWQ|1|A|A|19 interacts with 5NWQ|1|A|G|34
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5NWQ|1|A|A|19 interacts with 5NWQ|1|A|G|34
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  3 Initial     33 (1 insertion) and   19 (0 insertion)
pMakeNodes probed for insert:  a=5NWQ|1|A|G|34 B=5NWQ|1|A|A|19
pMakeNodes making a cluster near strand break a=5NWQ|1|A|G|34 B=5NWQ|1|A|A|19
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 6 to 7 and then 8 to 9
aa is 7 bb is 8
  4 Cluster   5NWQ|1|A|G|34:5NWQ|1|A|A|35 5NWQ|1|A|U|18:5NWQ|1|A|A|19
    LR Inter  5NWQ|1|A|G|34 5NWQ|1|A|U|18 tSH 
    LR Inter  5NWQ|1|A|A|35 5NWQ|1|A|U|18 cWW 
    LR Inter  5NWQ|1|A|G|34 5NWQ|1|A|A|19 cSW 
pMakeNodesCluster a=8 B=7 at the end
pMakeNodesCluster a=8 B=7 at the end
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 10
pMakeMotifModelFromSSF:   3   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   4   Cluster Left  6  7 Right  8  9
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5NWQ|1|A|A|30
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 0 0 0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GACA'
           RightLetter: 'C'
               Comment: ' // Cluster node 5NWQ|1|A|G|29:5NWQ|1|A|A|32 and 5NWQ|1|A|C|20:5NWQ|1|A|C|20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.2497

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 5NWQ|1|A|A|33 - 5NWQ|1|A|A|19 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5NWQ|1|A|A|30'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0641

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 7
             LeftIndex: [6 7]
            RightIndex: [8 9]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GA'
           RightLetter: 'UA'
               Comment: ' // Cluster node 5NWQ|1|A|G|34:5NWQ|1|A|A|35 and 5NWQ|1|A|U|18:5NWQ|1|A|A|19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0641

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 10
pMakeMotifModelFromSSF:   3   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   4     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   6   Cluster Left  6  7 Right  8  9
pMakeMotifModelFromSSF:   7   Initial Left  8 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 8
pUpdateModelWithSSF: IL_52743.1 allow insertions from initial node 7?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_52743.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.9423

Timestamp 18-Jul-2025 22:48:08
pMakeSCFGModels: Making JAR3D model for motif group IL_53448.1, number 212 of 411
pMakeNodes starting loop:     a=5BTM|1|A|C|19 B=5BTM|1|A|G|37
  2 Basepair    19   37 CG cWW 
No need to probe because of interaction between a=5BTM|1|A|U|20 B=5BTM|1|A|A|35
  3 Basepair    20   35 UA tWH 
pMakeNodes probe for inserts:  a=5BTM|1|A|A|21 B=5BTM|1|A|U|34
pMakeNodesProbeForInsertions:  a 5BTM|1|A|A|21 interacts with 5BTM|1|A|A|22
pMakeNodesProbeForInsertions:  B 5BTM|1|A|U|34 interacts with 5BTM|1|A|G|23
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 5BTM|1|A|U|34 interacts with 5BTM|1|A|G|23
pMakeNodes probed for insert:  a=5BTM|1|A|A|21 B=5BTM|1|A|U|34
pMakeNodes making a cluster near strand break a=5BTM|1|A|A|21 B=5BTM|1|A|U|34
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 5 and then 6 to 6
aa is 5 bb is 6
  4 Cluster   5BTM|1|A|A|21:5BTM|1|A|G|23 5BTM|1|A|U|34:5BTM|1|A|U|34
    LR Inter  5BTM|1|A|G|23 5BTM|1|A|U|34 cWW 
    LL Inter  5BTM|1|A|A|21 5BTM|1|A|A|22 cSH 
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C19 - G37 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U20 - A35 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4 5]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAG'
           RightLetter: 'U'
               Comment: ' // Cluster node 5BTM|1|A|A|21:5BTM|1|A|G|23 and 5BTM|1|A|U|34:5BTM|1|A|U|34'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 6
pUpdateModelWithSSF: IL_53448.1 allow insertions from initial node 5?
ans =

    0.9952    0.0046    0.0002


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9952    0.0046    0.0002


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_53448.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.0244
   -4.0244
   -4.0244
   -4.0244
   -4.0244
   -4.0244
   -4.0244
   -4.0244
   -4.0244
   -4.3465
   -4.0244

Timestamp 18-Jul-2025 22:48:08
pMakeSCFGModels: Making JAR3D model for motif group IL_53581.1, number 213 of 411
pMakeNodes starting loop:     a=6SY6|1|D|G|5 B=6SY6|1|D|C|35
  2 Basepair     5   35 GC cWW 
No need to probe because of interaction between a=6SY6|1|D|A|6 B=6SY6|1|D|A|34
  3 Basepair     6   34 AA tWW 
pMakeNodes probe for inserts:  a=6SY6|1|D|G|7 B=6SY6|1|D|A|33
    Insertion on left  6SY6|1|D|G|7
pMakeNodesProbeForInsertions:  a 6SY6|1|D|A|8 interacts with 6SY6|1|D|A|33
pMakeNodesProbeForInsertions:  B 6SY6|1|D|A|33 interacts with 6SY6|1|D|A|8
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6SY6|1|D|A|33 interacts with 6SY6|1|D|A|8
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6SY6|1|D|A|8 B=6SY6|1|D|A|33
  4 Basepair     8   33 AA tWH 
No need to probe because of interaction between a=6SY6|1|D|A|9 B=6SY6|1|D|A|32
pMakeNodes making a cluster near strand break a=6SY6|1|D|A|9 B=6SY6|1|D|A|32
pMakeNodesCluster: amax is 12 bmin is 13, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 12 and then 13 to 19
aa is 12 bb is 13
  5 Cluster   6SY6|1|D|A|9:6SY6|1|D|G|17 6SY6|1|D|C|26:6SY6|1|D|A|32
    LR Inter  6SY6|1|D|G|17 6SY6|1|D|C|26 cWW 
    LR Inter  6SY6|1|D|G|16 6SY6|1|D|A|27 cWW 
    LR Inter  6SY6|1|D|G|11 6SY6|1|D|G|28 tSS 
    LR Inter  6SY6|1|D|G|16 6SY6|1|D|G|28 bif 
    LR Inter  6SY6|1|D|U|10 6SY6|1|D|A|31 tWH 
    LR Inter  6SY6|1|D|A|9 6SY6|1|D|A|32 tWH 
    LR Inter  6SY6|1|D|G|17 6SY6|1|D|A|32 tSS 
    RR Inter  6SY6|1|D|A|27 6SY6|1|D|A|31 cSS 
    RR Inter  6SY6|1|D|C|26 6SY6|1|D|A|32 cSS 
    Left  strand conserved insertion 6SY6|1|D|U|12 at position 4
    Left  strand conserved insertion 6SY6|1|D|U|13 at position 5
    Left  strand conserved insertion 6SY6|1|D|A|14 at position 6
    Right strand conserved insertion 6SY6|1|D|A|29 at position 4
    Right strand conserved insertion 6SY6|1|D|G|30 at position 5
pMakeNodesCluster a=13 B=12 at the end
pMakeNodesCluster a=13 B=12 at the end
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 22
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 22
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 21
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right 20
pMakeMotifModelFromSSF:   5   Cluster Left  5  6  7  8  9 10 11 12 Right 13 14 15 16 17 18 19
pMakeMotifModelFromSSF:   6   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6SY6|1|D|G|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 22
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [22×22 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 22
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G5 - C35 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: 'A'
               Comment: ' // Basepair A6 - A34 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6SY6|1|D|G|7'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'AUGUUAGG'
           RightLetter: 'CAGAGAA'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×14 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: [1 2 3 4 5 6 7]
      InsertionComment: []
                IBases: [14×2 double]
    InteractionComment: {1×14 cell}
      JunctionDeletion: []
          InterIndices: [14×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [4 5 6]
         RightNotInter: [4 5]
              NormCons: 3.0092e-05

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A8 - A33 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [5 6 7 8 9 10 11 12]
            RightIndex: [13 14 15 16 17 18 19]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUGUUAGG'
           RightLetter: 'CAGAGAA'
               Comment: ' // Cluster node 6SY6|1|D|A|9:6SY6|1|D|G|17 and 6SY6|1|D|C|26:6SY6|1|D|A|32'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×14 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: [1 2 3 4 5 6 7]
      InsertionComment: []
                IBases: [14×2 double]
    InteractionComment: {1×14 cell}
      JunctionDeletion: []
          InterIndices: [14×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [4 5 6]
         RightNotInter: [4 5]
              NormCons: 3.0092e-05

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 22
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 22
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 21
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 20
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 20
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right 20
pMakeMotifModelFromSSF:   7   Cluster Left  5  6  7  8  9 10 11 12 Right 13 14 15 16 17 18 19
pMakeMotifModelFromSSF:   8   Initial Left 13 Right 12
pMakeMotifModelFromSSF:   9   Hairpin Left 13 Right 12
pNextNodeJunction: Found a hairpin at node 9
pUpdateModelWithSSF: IL_53581.1 allow insertions from initial node 8?
ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_53581.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.6695
   -7.6695

Timestamp 18-Jul-2025 22:48:09
pMakeSCFGModels: Making JAR3D model for motif group IL_53596.1, number 214 of 411
pMakeNodes starting loop:     a=6PMO|1|A|G|159 B=6PMO|1|A|C|186
  2 Basepair   159  186 GC cWW 
pMakeNodes probe for inserts:  a=6PMO|1|A|U|160 B=6PMO|1|A|U|185
    Insertion on left  6PMO|1|A|U|160
    Insertion on left  6PMO|1|A|G|161
    Insertion on left  6PMO|1|A|G|162
    Insertion on left  6PMO|1|A|A|163
    Insertion on left  6PMO|1|A|C|166
pMakeNodesProbeForInsertions:  a 6PMO|1|A|G|167 interacts with 6PMO|1|A|U|185
pMakeNodesProbeForInsertions:  B 6PMO|1|A|U|185 interacts with 6PMO|1|A|G|167
pMakeNodesProbeForInsertions:  B 6PMO|1|A|U|185 interacts with 6PMO|1|A|G|167
pMakeNodes probed for insert:  a=6PMO|1|A|G|167 B=6PMO|1|A|U|185
  3 Basepair   167  185 GU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6PMO|1|A|U|160
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6PMO|1|A|G|161
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6PMO|1|A|G|162
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6PMO|1|A|A|163
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6PMO|1|A|A|164
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUGGAC'
           RightLetter: 'C'
               Comment: ' // Basepair G159 - C186 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6PMO|1|A|U|160'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6PMO|1|A|G|161'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6PMO|1|A|G|162'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6PMO|1|A|A|163'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6PMO|1|A|A|164'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G167 - U185 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  12   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  13  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  14   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_53596.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.2788
   -7.2788

Timestamp 18-Jul-2025 22:48:09
pMakeSCFGModels: Making JAR3D model for motif group IL_53787.1, number 215 of 411
pMakeNodes starting loop:     a=3IGI|1|A|C|197 B=3IGI|1|A|G|169
  2 Basepair   197  169 CG cWW 
pMakeNodes probe for inserts:  a=3IGI|1|A|U|198 B=3IGI|1|A|U|168
    Insertion on left  3IGI|1|A|U|198
    Insertion on left  3IGI|1|A|U|199
    Insertion on left  3IGI|1|A|U|200
    Insertion on left  3IGI|1|A|C|201
    Insertion on left  3IGI|1|A|U|202
    Insertion on left  3IGI|1|A|G|203
    Insertion on left  3IGI|1|A|C|204
    Insertion on left  3IGI|1|A|C|205
    Insertion on left  3IGI|1|A|A|206
    Insertion on left  3IGI|1|A|A|208
pMakeNodesProbeForInsertions:  a 3IGI|1|A|G|209 interacts with 3IGI|1|A|U|168
pMakeNodesProbeForInsertions:  B 3IGI|1|A|U|168 interacts with 3IGI|1|A|G|209
pMakeNodesProbeForInsertions:  B 3IGI|1|A|U|168 interacts with 3IGI|1|A|G|209
pMakeNodes probed for insert:  a=3IGI|1|A|G|209 B=3IGI|1|A|U|168
  3 Basepair   209  168 GU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:   4   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|G|169
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|C|197
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|U|198
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|U|199
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|U|200
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|C|201
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|U|202
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|G|203
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|C|204
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|C|205
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-11 8.1893e-10 8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 … ]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CUUUCUGCCAA'
           RightLetter: 'G'
               Comment: ' // Basepair C197 - G169 cWW '
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Node 15

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Node 16

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Node 17

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Node 18

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Node 19

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Node 20

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Node 21

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Node 22

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 23

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 24

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pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 13
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 13
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 13
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 13
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 13
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 13
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 13
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 13
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 13
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 13
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 13
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 13
pMakeMotifModelFromSSF:  18   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  19     Fixed Left 10 Right 13
pMakeMotifModelFromSSF:  20   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  21     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  22   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  23  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  24   Hairpin Left 13 Right 12
pNextNodeJunction: Found a hairpin at node 24
pNextNodeJunction: Found a hairpin at node 24

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_53787.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.4803

Timestamp 18-Jul-2025 22:48:10
pMakeSCFGModels: Making JAR3D model for motif group IL_54041.2, number 216 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|G|799 B=5J7L|1|DA|C|678
  2 Basepair   799  678 GC cWW 
No need to probe because of interaction between a=5J7L|1|DA|A|800 B=5J7L|1|DA|A|677
  3 Basepair   800  677 AA tWW 
No need to probe because of interaction between a=5J7L|1|DA|A|802 B=5J7L|1|DA|A|676
  4 Basepair   802  676 AA tWH 
No need to probe because of interaction between a=5J7L|1|DA|U|803 B=5J7L|1|DA|A|675
  5 Basepair   803  675 UA tWH 
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|804 B=5J7L|1|DA|G|674
    Insertion on left  5J7L|1|DA|A|804
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|C|806 interacts with 5J7L|1|DA|G|674
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|674 interacts with 5J7L|1|DA|C|806
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|674 interacts with 5J7L|1|DA|C|806
pMakeNodes probed for insert:  a=5J7L|1|DA|C|806 B=5J7L|1|DA|G|674
  6 Basepair   806  674 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|678
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G799 - C678 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A800 - A677 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A802 - A676 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: 'A'
               Comment: ' // Basepair U803 - A675 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|678'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C806 - G674 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_54041.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0504
   -6.0504
   -6.0504
   -6.0504
   -9.6825
   -9.6825
  -10.6325

Timestamp 18-Jul-2025 22:48:10
pMakeSCFGModels: Making JAR3D model for motif group IL_54050.1, number 217 of 411
pMakeNodes starting loop:     a=4KR6|1|D|U|8 B=4KR6|1|D|G|28
  2 Basepair     8   28 UG cWW 
pMakeNodes probe for inserts:  a=4KR6|1|D|A|9 B=4KR6|1|D|A|27
    Insertion on left  4KR6|1|D|A|9
    Insertion on left  4KR6|1|D|U|13
    Insertion on left  4KR6|1|D|C|14
    Insertion on left  4KR6|1|D|C|15
pMakeNodesProbeForInsertions:  a 4KR6|1|D|U|16 interacts with 4KR6|1|D|A|27
pMakeNodesProbeForInsertions:  B 4KR6|1|D|A|27 interacts with 4KR6|1|D|U|16
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4KR6|1|D|A|27 interacts with 4KR6|1|D|U|16
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4KR6|1|D|U|16 B=4KR6|1|D|A|27
  3 Basepair    16   27 UA cWW 
pMakeNodes probe for inserts:  a=4KR6|1|D|G|18 B=4KR6|1|D|A|26
    Insertion on right 4KR6|1|D|A|26
pMakeNodesProbeForInsertions:  a 4KR6|1|D|G|18 interacts with 4KR6|1|D|C|25
pMakeNodesProbeForInsertions:  B 4KR6|1|D|C|25 interacts with 4KR6|1|D|G|18
pMakeNodesProbeForInsertions:  B 4KR6|1|D|C|25 interacts with 4KR6|1|D|G|18
pMakeNodes probed for insert:  a=4KR6|1|D|G|18 B=4KR6|1|D|C|25
  4 Basepair    18   25 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KR6|1|D|A|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KR6|1|D|G|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KR6|1|D|U|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KR6|1|D|G|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4KR6|1|D|U|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UAUCC'
           RightLetter: 'G'
               Comment: ' // Basepair U8 - G28 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4KR6|1|D|A|9'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4KR6|1|D|G|10'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4KR6|1|D|U|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4KR6|1|D|G|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'AA'
               Comment: ' // Basepair U16 - A27 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4KR6|1|D|U|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G18 - C25 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right 10
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  13   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  14  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  15   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a hairpin at node 15

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_54050.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.4862

Timestamp 18-Jul-2025 22:48:11
pMakeSCFGModels: Making JAR3D model for motif group IL_54177.4, number 218 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|G|562 B=8P9A|1|sR|C|583
  2 Basepair   562  583 GC cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|U|563 B=8P9A|1|sR|A|580
    Insertion on left  8P9A|1|sR|U|563
    Insertion on left  8P9A|1|sR|G|564
    Insertion on left  8P9A|1|sR|C|565
    Insertion on left  8P9A|1|sR|C|566
    Insertion on right 8P9A|1|sR|A|580
    Insertion on right 8P9A|1|sR|U|578
    Insertion on right 8P9A|1|sR|G|577
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|A|567 interacts with 8P9A|1|sR|G|576
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|G|576 interacts with 8P9A|1|sR|A|567
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|G|576 interacts with 8P9A|1|sR|A|567
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|sR|A|567 B=8P9A|1|sR|G|576
  3 Basepair   567  576 AG tHS 
No need to probe because of interaction between a=8P9A|1|sR|G|568 B=8P9A|1|sR|C|575
  4 Basepair   568  575 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|U|563
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|G|564
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|C|565
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|C|566
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|A|579
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|U|578
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|G|577
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUGCC'
           RightLetter: 'GUAC'
               Comment: ' // Basepair G562 - C583 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|U|563'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|G|564'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|C|565'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|C|566'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|A|579'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|U|578'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|G|577'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A567 - G576 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 19
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G568 - C575 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 21
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  12   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  13     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  14   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  15     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  16   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  17  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  18  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  19   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Found a hairpin at node 19

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_54177.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.3135
   -5.3135
   -6.2690
   -6.2690

Timestamp 18-Jul-2025 22:48:11
pMakeSCFGModels: Making JAR3D model for motif group IL_54737.1, number 219 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|2103 B=5J7L|1|DA|G|2186
  2 Basepair  2103 2186 CG cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|C|2104 B=5J7L|1|DA|U|2185
    Insertion on left  5J7L|1|DA|C|2104
    Insertion on right 5J7L|1|DA|U|2185
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|U|2105 interacts with 5J7L|1|DA|A|2184
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|2184 interacts with 5J7L|1|DA|U|2105
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|2184 interacts with 5J7L|1|DA|U|2105
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5J7L|1|DA|U|2105 B=5J7L|1|DA|A|2184
  3 Basepair  2105 2184 UA tHS 
No need to probe because of interaction between a=5J7L|1|DA|U|2106 B=5J7L|1|DA|A|2183
  4 Basepair  2106 2183 UA cWW 
No need to probe because of interaction between a=5J7L|1|DA|G|2107 B=5J7L|1|DA|U|2182
  5 Basepair  2107 2182 GU cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|2108 B=5J7L|1|DA|U|2181
    Insertion on left  5J7L|1|DA|A|2108
    Insertion on left  5J7L|1|DA|U|2109
    Insertion on left  5J7L|1|DA|G|2110
    Insertion on left  5J7L|1|DA|G|2112
    Insertion on left  5J7L|1|DA|U|2113
    Insertion on right 5J7L|1|DA|U|2181
    Insertion on right 5J7L|1|DA|U|2180
    Insertion on right 5J7L|1|DA|C|2179
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|G|2120 interacts with 5J7L|1|DA|C|2178
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|2178 interacts with 5J7L|1|DA|G|2120
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|2178 interacts with 5J7L|1|DA|G|2120
pMakeNodes probed for insert:  a=5J7L|1|DA|G|2120 B=5J7L|1|DA|C|2178
  6 Basepair  2120 2178 GC cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 20
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 18
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right 17
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right 16
pMakeMotifModelFromSSF:   6  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:   7   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|2104
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|C|2178
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|2108
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|U|2109
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2110
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|U|2111
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2112
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|A|2117
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|G|2116
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|G|2115
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 20
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [20×20 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CC'
           RightLetter: 'UG'
               Comment: ' // Basepair C2103 - G2186 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|2104'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|C|2178'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U2105 - A2184 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U2106 - A2183 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAUGGU'
           RightLetter: 'CUUU'
               Comment: ' // Basepair G2107 - U2182 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|2108'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|U|2109'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 15
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        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|2110'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 15
             Insertion: []
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        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
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               Comment: ' // Fixed node on left for 5J7L|1|DA|U|2111'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 10
            RightIndex: 15
             Insertion: []
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        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|2112'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 11
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             LeftIndex: 11
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|A|2117'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 23
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|G|2116'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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                  lpar: []
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Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 25
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|G|2115'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: []
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Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 26
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 27
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2120 - C2178 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 30
             LeftIndex: 12
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 20
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 19
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 19
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 19
pMakeMotifModelFromSSF:   6   Initial Left  3 Right 18
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right 18
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right 17
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right 16
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 15
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 15
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 15
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 15
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 15
pMakeMotifModelFromSSF:  16     Fixed Left  9 Right 15
pMakeMotifModelFromSSF:  17   Initial Left 10 Right 15
pMakeMotifModelFromSSF:  18     Fixed Left 10 Right 15
pMakeMotifModelFromSSF:  19   Initial Left 11 Right 15
pMakeMotifModelFromSSF:  20     Fixed Left 11 Right 15
pMakeMotifModelFromSSF:  21   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  22     Fixed Left 11 Right 14
pMakeMotifModelFromSSF:  23   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  24     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  25   Initial Left 11 Right 12
pMakeMotifModelFromSSF:  26  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  27   Hairpin Left 12 Right 11
pNextNodeJunction: Found a hairpin at node 27
pNextNodeJunction: Found a hairpin at node 27

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_54737.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -20.9955

Timestamp 18-Jul-2025 22:48:12
pMakeSCFGModels: Making JAR3D model for motif group IL_54896.1, number 220 of 411
pMakeNodes starting loop:     a=4XWF|1|A|U|11 B=4XWF|1|A|G|35
  2 Basepair    11   35 UG cWW 
pMakeNodes probe for inserts:  a=4XWF|1|A|G|12 B=4XWF|1|A|G|34
    Insertion on left  4XWF|1|A|G|12
    Insertion on left  4XWF|1|A|G|13
    Insertion on left  4XWF|1|A|C|14
    Insertion on left  4XWF|1|A|G|15
    Insertion on left  4XWF|1|A|A|17
    Insertion on left  4XWF|1|A|C|18
    Insertion on left  4XWF|1|A|A|19
    Insertion on right 4XWF|1|A|G|34
pMakeNodesProbeForInsertions:  a 4XWF|1|A|G|20 interacts with 4XWF|1|A|C|33
pMakeNodesProbeForInsertions:  B 4XWF|1|A|C|33 interacts with 4XWF|1|A|G|20
pMakeNodesProbeForInsertions:  B 4XWF|1|A|C|33 interacts with 4XWF|1|A|G|20
pMakeNodes probed for insert:  a=4XWF|1|A|G|20 B=4XWF|1|A|C|33
  3 Basepair    20   33 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   4   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4XWF|1|A|G|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4XWF|1|A|G|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4XWF|1|A|C|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4XWF|1|A|G|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4XWF|1|A|A|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4XWF|1|A|A|17
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4XWF|1|A|C|18
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4XWF|1|A|C|33
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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                 Right: []
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                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGGCGACA'
           RightLetter: 'GG'
               Comment: ' // Basepair U11 - G35 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4XWF|1|A|G|12'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4XWF|1|A|G|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4XWF|1|A|C|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4XWF|1|A|G|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4XWF|1|A|A|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4XWF|1|A|A|17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                  lpar: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4XWF|1|A|C|18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4XWF|1|A|C|33'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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                  lpar: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                  lpar: []
                  rpar: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G20 - C33 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 22
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 11
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  19  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  20   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Found a hairpin at node 20

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_54896.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.0456

Timestamp 18-Jul-2025 22:48:12
pMakeSCFGModels: Making JAR3D model for motif group IL_55516.2, number 221 of 411
pMakeNodes starting loop:     a=6DME|1|A|G|33 B=6DME|1|A|C|22
  2 Basepair    33   22 GC cWW 
No need to probe because of interaction between a=6DME|1|A|A|34 B=6DME|1|A|A|21
  3 Basepair    34   21 AA cWW 
pMakeNodes probe for inserts:  a=6DME|1|A|A|35 B=6DME|1|A|C|20
pMakeNodesProbeForInsertions:  a 6DME|1|A|A|35 interacts with 6DME|1|A|G|36
pMakeNodesProbeForInsertions:  B 6DME|1|A|C|20 interacts with 6DME|1|A|G|36
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 6DME|1|A|C|20 interacts with 6DME|1|A|G|36
pMakeNodes probed for insert:  a=6DME|1|A|A|35 B=6DME|1|A|C|20
pMakeNodes making a cluster near strand break a=6DME|1|A|A|35 B=6DME|1|A|C|20
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 4 and then 5 to 5
aa is 4 bb is 5
  4 Cluster   6DME|1|A|A|35:6DME|1|A|G|36 6DME|1|A|C|20:6DME|1|A|C|20
    LR Inter  6DME|1|A|G|36 6DME|1|A|C|20 cWW 
    LL Inter  6DME|1|A|A|35 6DME|1|A|G|36 cSH 
pMakeNodesCluster a=5 B=4 at the end
pMakeNodesCluster a=5 B=4 at the end
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Cluster Left  3  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G33 - C22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A34 - A21 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4]
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AG'
           RightLetter: 'C'
               Comment: ' // Cluster node 6DME|1|A|A|35:6DME|1|A|G|36 and 6DME|1|A|C|20:6DME|1|A|C|20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2520

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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         RightNotInter: []
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  6
pMakeMotifModelFromSSF:   4   Cluster Left  3  4 Right  5
pMakeMotifModelFromSSF:   5   Initial Left  5 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pUpdateModelWithSSF: IL_55516.2 allow insertions from initial node 5?
ans =

    0.9923    0.0073    0.0004


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9923    0.0073    0.0004


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_55516.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.5277
   -6.5551
   -6.1092
   -5.6175
   -5.6175
   -9.7277
   -8.1729

Timestamp 18-Jul-2025 22:48:13
pMakeSCFGModels: Making JAR3D model for motif group IL_55917.1, number 222 of 411
pMakeNodes starting loop:     a=4KR9|1|M|U|8 B=4KR9|1|M|G|28
  2 Basepair     8   28 UG cWW 
pMakeNodes probe for inserts:  a=4KR9|1|M|A|9 B=4KR9|1|M|A|27
    Insertion on left  4KR9|1|M|A|9
    Insertion on left  4KR9|1|M|G|10
    Insertion on left  4KR9|1|M|U|13
    Insertion on left  4KR9|1|M|C|15
pMakeNodesProbeForInsertions:  a 4KR9|1|M|U|16 interacts with 4KR9|1|M|A|27
pMakeNodesProbeForInsertions:  B 4KR9|1|M|A|27 interacts with 4KR9|1|M|U|16
pMakeNodesProbeForInsertions:  B 4KR9|1|M|A|27 interacts with 4KR9|1|M|U|16
pMakeNodes probed for insert:  a=4KR9|1|M|U|16 B=4KR9|1|M|A|27
  3 Basepair    16   27 UA cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KR9|1|M|A|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KR9|1|M|G|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KR9|1|M|U|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4KR9|1|M|G|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UAGUC'
           RightLetter: 'G'
               Comment: ' // Basepair U8 - G28 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4KR9|1|M|A|9'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4KR9|1|M|G|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4KR9|1|M|U|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4KR9|1|M|G|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U16 - A27 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  12   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_55917.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2822

Timestamp 18-Jul-2025 22:48:13
pMakeSCFGModels: Making JAR3D model for motif group IL_55953.3, number 223 of 411
pMakeNodes starting loop:     a=4QK9|1|A|G|29 B=4QK9|1|A|C|103
  2 Basepair    29  103 GC cWW 
No need to probe because of interaction between a=4QK9|1|A|G|30 B=4QK9|1|A|A|102
  3 Basepair    30  102 GA tSH 
pMakeNodes probe for inserts:  a=4QK9|1|A|A|31 B=4QK9|1|A|A|101
    Insertion on right 4QK9|1|A|A|101
pMakeNodesProbeForInsertions:  a 4QK9|1|A|A|31 interacts with 4QK9|1|A|U|100
pMakeNodesProbeForInsertions:  B 4QK9|1|A|U|100 interacts with 4QK9|1|A|A|31
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4QK9|1|A|U|100 interacts with 4QK9|1|A|A|31
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4QK9|1|A|A|31 B=4QK9|1|A|U|100
  4 Basepair    31  100 AU tHS 
pMakeNodes probe for inserts:  a=4QK9|1|A|C|32 B=4QK9|1|A|C|99
    Insertion on left  4QK9|1|A|C|32
pMakeNodesProbeForInsertions:  a 4QK9|1|A|C|33 interacts with 4QK9|1|A|C|99
pMakeNodesProbeForInsertions:  B 4QK9|1|A|C|99 interacts with 4QK9|1|A|C|33
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4QK9|1|A|C|99 interacts with 4QK9|1|A|C|33
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4QK9|1|A|C|33 B=4QK9|1|A|C|99
  5 Basepair    33   99 CC bif 
No need to probe because of interaction between a=4QK9|1|A|C|34 B=4QK9|1|A|G|98
  6 Basepair    34   98 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4QK9|1|A|A|101
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4QK9|1|A|C|32
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G29 - C103 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'AA'
               Comment: ' // Basepair G30 - A102 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4QK9|1|A|A|101'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AC'
           RightLetter: 'U'
               Comment: ' // Basepair A31 - U100 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4QK9|1|A|C|32'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C33 - C99 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C34 - G98 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_55953.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.4409
   -4.4409
   -5.2882
   -4.4409

Timestamp 18-Jul-2025 22:48:14
pMakeSCFGModels: Making JAR3D model for motif group IL_56317.1, number 224 of 411
pMakeNodes starting loop:     a=8CRE|1|1|G|1807 B=8CRE|1|1|C|1627
  2 Basepair  1807 1627 GC cWW 
pMakeNodes probe for inserts:  a=8CRE|1|1|G|1808 B=8CRE|1|1|U|1626
    Insertion on left  8CRE|1|1|G|1808
    Insertion on right 8CRE|1|1|U|1626
    Insertion on right 8CRE|1|1|C|1624
pMakeNodesProbeForInsertions:  a 8CRE|1|1|A|1809 interacts with 8CRE|1|1|U|1623
pMakeNodesProbeForInsertions:  B 8CRE|1|1|U|1623 interacts with 8CRE|1|1|A|1809
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8CRE|1|1|U|1623 interacts with 8CRE|1|1|A|1812
pMakeNodes probed for insert:  a=8CRE|1|1|A|1809 B=8CRE|1|1|U|1623
pMakeNodes making a cluster near strand break a=8CRE|1|1|A|1809 B=8CRE|1|1|U|1623
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 5 and then 6 to 6
aa is 5 bb is 6
  3 Cluster   8CRE|1|1|A|1809:8CRE|1|1|A|1812 8CRE|1|1|U|1623:8CRE|1|1|U|1623
    LR Inter  8CRE|1|1|A|1809 8CRE|1|1|U|1623 tHS 
    LR Inter  8CRE|1|1|A|1812 8CRE|1|1|U|1623 cWW 
    Left  strand conserved insertion 8CRE|1|1|A|1810 at position 2
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  3  4  5 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|C|1624
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|1|A|1809
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|1|G|1808
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: 'CUC'
               Comment: ' // Basepair G1807 - C1627 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|C|1624'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2507

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|1|A|1809'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|1|G|1808'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 10
             LeftIndex: [3 4 5]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAA'
           RightLetter: 'U'
               Comment: ' // Cluster node 8CRE|1|1|A|1809:8CRE|1|1|A|1812 and 8CRE|1|1|U|1623:8CRE|1|1|U|1623'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2507

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   7     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   9   Cluster Left  3  4  5 Right  6
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  5
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 11
pUpdateModelWithSSF: IL_56317.1 allow insertions from initial node 10?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_56317.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1986
   -6.1986

Timestamp 18-Jul-2025 22:48:14
pMakeSCFGModels: Making JAR3D model for motif group IL_56455.6, number 225 of 411
pMakeNodes starting loop:     a=1DFU|1|M|C|97 B=1DFU|1|N|G|79
  2 Basepair    97   79 CG cWW 
No need to probe because of interaction between a=1DFU|1|M|G|98 B=1DFU|1|N|A|78
  3 Basepair    98   78 GA tSH 
No need to probe because of interaction between a=1DFU|1|M|A|99 B=1DFU|1|N|U|77
  4 Basepair    99   77 AU tHW 
No need to probe because of interaction between a=1DFU|1|M|G|100 B=1DFU|1|N|G|76
  5 Basepair   100   76 GG bif 
No need to probe because of interaction between a=1DFU|1|M|A|101 B=1DFU|1|N|G|75
  6 Basepair   101   75 AG wat 
No need to probe because of interaction between a=1DFU|1|M|G|102 B=1DFU|1|N|U|74
  7 Basepair   102   74 GU bif 
No need to probe because of interaction between a=1DFU|1|M|U|103 B=1DFU|1|N|A|73
  8 Basepair   103   73 UA tWH 
No need to probe because of interaction between a=1DFU|1|M|A|104 B=1DFU|1|N|G|72
  9 Basepair   104   72 AG tHS 
No need to probe because of interaction between a=1DFU|1|M|G|105 B=1DFU|1|N|C|71
 10 Basepair   105   71 GC cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 16
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 15
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right 14
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right 13
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C97 - G79 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G98 - A78 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A99 - U77 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G100 - G76 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A101 - G75 wat '
              NumLoops: []
                  Edge: 14
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G102 - U74 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U103 - A73 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A104 - G72 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G105 - C71 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 17
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 16
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 15
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right 14
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right 13
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_56455.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.6474
   -9.6474
   -9.6474
   -9.6474
   -9.7805
  -10.7106
   -9.6474

Timestamp 18-Jul-2025 22:48:15
pMakeSCFGModels: Making JAR3D model for motif group IL_56987.1, number 226 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|G|930 B=5J7L|1|DA|C|848
  2 Basepair   930  848 GC cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|U|932 B=5J7L|1|DA|U|847||A
    Insertion on left  5J7L|1|DA|U|932
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|A|933 interacts with 5J7L|1|DA|U|847||A
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|U|847||A interacts with 5J7L|1|DA|A|933
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|U|847||A interacts with 5J7L|1|DA|A|933
pMakeNodes probed for insert:  a=5J7L|1|DA|A|933 B=5J7L|1|DA|U|847||A
  3 Basepair   933  847 AU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|848
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GU'
           RightLetter: 'C'
               Comment: ' // Basepair G930 - C848 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|848'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A933 - U847 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_56987.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.1600
   -4.2063
   -4.6678

Timestamp 18-Jul-2025 22:48:15
pMakeSCFGModels: Making JAR3D model for motif group IL_57188.5, number 227 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|C|1018 B=9DFE|1|1A|G|1144
  2 Basepair  1018 1144 CG cWW 
No need to probe because of interaction between a=9DFE|1|1A|U|1019 B=9DFE|1|1A|A|1142|||A
pMakeNodes making a cluster near strand break a=9DFE|1|1A|U|1019 B=9DFE|1|1A|A|1142|||A
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 9 to 10
aa is 4 bb is 9
  3 Cluster   9DFE|1|1A|U|1019:9DFE|1|1A|A|1021 9DFE|1|1A|U|1141:9DFE|1|1A|A|1142|||A
    LR Inter  9DFE|1|1A|A|1021 9DFE|1|1A|U|1141 tWW 
    LR Inter  9DFE|1|1A|U|1019 9DFE|1|1A|A|1142|||A tWW 
    LL Inter  9DFE|1|1A|U|1019 9DFE|1|1A|A|1021 cSH 
    Left  strand conserved insertion 9DFE|1|1A|A|1020 at position 2
pMakeNodesCluster a=5 B=8 at the end
pMakeNodesCluster a=5 B=8 at the end
pMakeNodes probe for inserts:  a=9DFE|1|1A|G|1022 B=9DFE|1|1A|C|1140
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|G|1022 interacts with 9DFE|1|1A|U|1023
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|C|1140 interacts with 9DFE|1|1A|G|1024
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|C|1140 interacts with 9DFE|1|1A|G|1024
  4 Initial   1022 (0 insertion) and 1140 (0 insertion)
pMakeNodes probed for insert:  a=9DFE|1|1A|G|1022 B=9DFE|1|1A|C|1140
pMakeNodes making a cluster near strand break a=9DFE|1|1A|G|1022 B=9DFE|1|1A|C|1140
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 7 and then 8 to 8
aa is 7 bb is 8
  5 Cluster   9DFE|1|1A|G|1022:9DFE|1|1A|G|1024 9DFE|1|1A|C|1140:9DFE|1|1A|C|1140
    LR Inter  9DFE|1|1A|G|1024 9DFE|1|1A|C|1140 cWW 
    LL Inter  9DFE|1|1A|G|1022 9DFE|1|1A|U|1023 cSH 
pMakeNodesCluster a=8 B=7 at the end
pMakeNodesCluster a=8 B=7 at the end
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  9 10
pMakeMotifModelFromSSF:   4   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   5   Cluster Left  5  6  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1018 - G1144 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4]
            RightIndex: [9 10]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAA'
           RightLetter: 'UA'
               Comment: ' // Cluster node 9DFE|1|1A|U|1019:9DFE|1|1A|A|1021 and 9DFE|1|1A|U|1141:9DFE|1|1A|A|1142|||A'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.0712

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 9DFE|1|1A|G|1022 - 9DFE|1|1A|C|1140 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [5 6 7]
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUG'
           RightLetter: 'C'
               Comment: ' // Cluster node 9DFE|1|1A|G|1022:9DFE|1|1A|G|1024 and 9DFE|1|1A|C|1140:9DFE|1|1A|C|1140'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  9 10
pMakeMotifModelFromSSF:   4   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   5   Cluster Left  5  6  7 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  8 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 7
pUpdateModelWithSSF: IL_57188.5 allow insertions from initial node 6?
ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_57188.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.5027
   -6.9424
   -6.6464
   -6.6464
   -8.0905

Timestamp 18-Jul-2025 22:48:16
pMakeSCFGModels: Making JAR3D model for motif group IL_57741.1, number 228 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|C|910 B=8P9A|1|sR|G|899
pMakeNodes making a cluster near strand break a=8P9A|1|sR|C|910 B=8P9A|1|sR|G|899
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 14 to 16
aa is 5 bb is 14
  2 Cluster   8P9A|1|sR|C|910:8P9A|1|sR|A|915 8P9A|1|sR|C|897:8P9A|1|sR|G|899
    LR Inter  8P9A|1|sR|A|915 8P9A|1|sR|C|897 tHW 
    LR Inter  8P9A|1|sR|G|914 8P9A|1|sR|A|898 tSH 
    LR Inter  8P9A|1|sR|C|910 8P9A|1|sR|G|899 cWW 
    LL Inter  8P9A|1|sR|C|910 8P9A|1|sR|A|915 cSS 
    Left  strand conserved insertion 8P9A|1|sR|U|911 at position 2
    Left  strand conserved insertion 8P9A|1|sR|U|912 at position 3
pMakeNodesCluster a=6 B=13 at the end
pMakeNodesCluster a=6 B=13 at the end
pMakeNodes probe for inserts:  a=8P9A|1|sR|U|916 B=8P9A|1|sR|U|896
    Insertion on left  8P9A|1|sR|U|916
    Insertion on right 8P9A|1|sR|U|896
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|U|917 interacts with 8P9A|1|sR|G|895
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|G|895 interacts with 8P9A|1|sR|U|917
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|G|895 interacts with 8P9A|1|sR|U|917
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  3 Initial    916 (1 insertion) and  896 (1 insertion)
pMakeNodes probed for insert:  a=8P9A|1|sR|U|917 B=8P9A|1|sR|G|895
  4 Basepair   917  895 UG cWW 
No need to probe because of interaction between a=8P9A|1|sR|U|918 B=8P9A|1|sR|U|894
  5 Basepair   918  894 UU cWW 
No need to probe because of interaction between a=8P9A|1|sR|A|919 B=8P9A|1|sR|U|893
  6 Basepair   919  893 AU cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 14 15 16
pMakeMotifModelFromSSF:   3   Initial Left  6 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:   6  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   7   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|A|898
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|A|915
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: [14 15 16]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUUGA'
           RightLetter: 'CAG'
               Comment: ' // Cluster node 8P9A|1|sR|C|910:8P9A|1|sR|A|915 and 8P9A|1|sR|C|897:8P9A|1|sR|G|899'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.0701
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Initial node 8P9A|1|sR|U|916 - 8P9A|1|sR|U|896 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|A|898'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|A|915'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U917 - G895 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U918 - U894 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A919 - U893 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 14 15 16
pMakeMotifModelFromSSF:   3   Initial Left  6 Right 13
pMakeMotifModelFromSSF:   4     Fixed Left  6 Right 13
pMakeMotifModelFromSSF:   5   Initial Left  7 Right 13
pMakeMotifModelFromSSF:   6     Fixed Left  7 Right 13
pMakeMotifModelFromSSF:   7   Initial Left  7 Right 12
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_57741.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.7017

Timestamp 18-Jul-2025 22:48:17
pMakeSCFGModels: Making JAR3D model for motif group IL_57744.1, number 229 of 411
pMakeNodes starting loop:     a=5T3K|1|A|G|7 B=5T3K|1|B|C|28
  2 Basepair     7   28 GC cWW 
No need to probe because of interaction between a=5T3K|1|A|A|8 B=5T3K|1|B|A|27
  3 Basepair     8   27 AA cWW 
No need to probe because of interaction between a=5T3K|1|A|G|10 B=5T3K|1|B|C|26
  4 Basepair    10   26 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G7 - C28 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A8 - A27 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G10 - C26 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_57744.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.5795
   -4.9111
   -4.9111
   -9.1206
   -6.2477
   -7.1134
   -6.5024
   -8.5556
   -7.7988
   -5.5795
   -5.7613
   -6.0723
   -5.3245
   -5.2841
   -5.3245
   -7.1534
   -5.3464
   -5.3464
   -5.3464
   -5.3464
   -9.0402
   -6.0723

Timestamp 18-Jul-2025 22:48:17
pMakeSCFGModels: Making JAR3D model for motif group IL_57881.1, number 230 of 411
pMakeNodes starting loop:     a=4V9F|1|0|C|880 B=4V9F|1|0|G|870
  2 Basepair   880  870 CG cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|U|883 B=4V9F|1|0|G|868
    Insertion on left  4V9F|1|0|U|883
pMakeNodesProbeForInsertions:  a 4V9F|1|0|C|884 interacts with 4V9F|1|0|G|868
pMakeNodesProbeForInsertions:  B 4V9F|1|0|G|868 interacts with 4V9F|1|0|C|884
pMakeNodesProbeForInsertions:  B 4V9F|1|0|G|868 interacts with 4V9F|1|0|C|884
pMakeNodes probed for insert:  a=4V9F|1|0|C|884 B=4V9F|1|0|G|868
  3 Basepair   884  868 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|G|869
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CU'
           RightLetter: 'G'
               Comment: ' // Basepair C880 - G870 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|G|869'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C884 - G868 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_57881.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.5784

Timestamp 18-Jul-2025 22:48:18
pMakeSCFGModels: Making JAR3D model for motif group IL_58103.11, number 231 of 411
pMakeNodes starting loop:     a=4V9F|1|9|U|33 B=4V9F|1|9|A|47
pMakeNodes making a cluster near strand break a=4V9F|1|9|U|33 B=4V9F|1|9|A|47
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 4 and then 10 to 10
aa is 4 bb is 10
  2 Cluster   4V9F|1|9|U|33:4V9F|1|9|C|36 4V9F|1|9|A|47:4V9F|1|9|A|47
    LR Inter  4V9F|1|9|U|33 4V9F|1|9|A|47 cWW 
    LR Inter  4V9F|1|9|C|36 4V9F|1|9|A|47 cWS 
    Left  strand conserved insertion 4V9F|1|9|A|34 at position 2
    Left  strand conserved insertion 4V9F|1|9|C|35 at position 3
pMakeNodesCluster a=5 B=9 at the end
pMakeNodesCluster a=5 B=9 at the end
pMakeNodes probe for inserts:  a=4V9F|1|9|C|37 B=4V9F|1|9|C|46
pMakeNodesProbeForInsertions:  a 4V9F|1|9|C|37 interacts with 4V9F|1|9|G|43
pMakeNodesProbeForInsertions:  B 4V9F|1|9|C|46 interacts with 4V9F|1|9|G|43
pMakeNodesProbeForInsertions:  B 4V9F|1|9|C|46 interacts with 4V9F|1|9|G|43
  3 Initial     37 (0 insertion) and   46 (0 insertion)
pMakeNodes probed for insert:  a=4V9F|1|9|C|37 B=4V9F|1|9|C|46
pMakeNodes making a cluster near strand break a=4V9F|1|9|C|37 B=4V9F|1|9|C|46
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 5 and then 6 to 9
aa is 5 bb is 6
  4 Cluster   4V9F|1|9|C|37:4V9F|1|9|C|37 4V9F|1|9|G|43:4V9F|1|9|C|46
    LR Inter  4V9F|1|9|C|37 4V9F|1|9|G|43 cWW 
    RR Inter  4V9F|1|9|G|43 4V9F|1|9|C|46 tSW 
    Right strand conserved insertion 4V9F|1|9|A|44 at position 2
    Right strand conserved insertion 4V9F|1|9|A|45 at position 3
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 10
pMakeMotifModelFromSSF:   3   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   4   Cluster Left  5 Right  6  7  8  9
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UACC'
           RightLetter: 'A'
               Comment: ' // Cluster node 4V9F|1|9|U|33:4V9F|1|9|C|36 and 4V9F|1|9|A|47:4V9F|1|9|A|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.2458

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|9|C|37 - 4V9F|1|9|C|46 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: 5
            RightIndex: [6 7 8 9]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'C'
           RightLetter: 'GAAC'
               Comment: ' // Cluster node 4V9F|1|9|C|37:4V9F|1|9|C|37 and 4V9F|1|9|G|43:4V9F|1|9|C|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [2 3]
              NormCons: 0.2526

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4 Right 10
pMakeMotifModelFromSSF:   3   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   4   Cluster Left  5 Right  6  7  8  9
pMakeMotifModelFromSSF:   5   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 6
pUpdateModelWithSSF: IL_58103.11 allow insertions from initial node 5?
ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9980    0.0020    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_58103.11_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.0236
   -2.7703
   -3.1763
   -3.9425
   -4.3945
   -3.1763
   -2.7703
   -2.7703
   -2.7703

Timestamp 18-Jul-2025 22:48:18
pMakeSCFGModels: Making JAR3D model for motif group IL_58112.2, number 232 of 411
pMakeNodes starting loop:     a=4PMI|1|A|G|46 B=4PMI|1|A|C|74
  2 Basepair    46   74 GC cWW 
No need to probe because of interaction between a=4PMI|1|A|G|47 B=4PMI|1|A|A|73
  3 Basepair    47   73 GA cWW 
No need to probe because of interaction between a=4PMI|1|A|G|48 B=4PMI|1|A|G|71
  4 Basepair    48   71 GG tWW 
No need to probe because of interaction between a=4PMI|1|A|C|49 B=4PMI|1|A|G|70
  5 Basepair    49   70 CG cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G46 - C74 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G47 - A73 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G48 - G71 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C49 - G70 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_58112.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.0700
   -7.2193
   -7.4149
  -11.6680

Timestamp 18-Jul-2025 22:48:19
pMakeSCFGModels: Making JAR3D model for motif group IL_58126.1, number 233 of 411
pMakeNodes starting loop:     a=6VMY|1|A|C|326 B=6VMY|1|A|G|348
  2 Basepair   326  348 CG cWW 
pMakeNodes probe for inserts:  a=6VMY|1|A|A|327 B=6VMY|1|A|U|347
    Insertion on left  6VMY|1|A|A|327
pMakeNodesProbeForInsertions:  a 6VMY|1|A|C|328 interacts with 6VMY|1|A|U|347
pMakeNodesProbeForInsertions:  B 6VMY|1|A|U|347 interacts with 6VMY|1|A|C|328
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6VMY|1|A|U|347 interacts with 6VMY|1|A|C|328
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6VMY|1|A|C|328 B=6VMY|1|A|U|347
  3 Basepair   328  347 CU cWW 
No need to probe because of interaction between a=6VMY|1|A|G|329 B=6VMY|1|A|A|346
  4 Basepair   329  346 GA tHW 
No need to probe because of interaction between a=6VMY|1|A|A|330 B=6VMY|1|A|G|345
  5 Basepair   330  345 AG tHW 
No need to probe because of interaction between a=6VMY|1|A|A|331 B=6VMY|1|A|A|344
  6 Basepair   331  344 AA tHW 
No need to probe because of interaction between a=6VMY|1|A|U|332 B=6VMY|1|A|C|343
  7 Basepair   332  343 UC bif 
No need to probe because of interaction between a=6VMY|1|A|U|333 B=6VMY|1|A|A|342
  8 Basepair   333  342 UA cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right 13
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right 12
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   9   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6VMY|1|A|A|327
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: 'G'
               Comment: ' // Basepair C326 - G348 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6VMY|1|A|A|327'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'U'
               Comment: ' // Basepair C328 - U347 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G329 - A346 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A330 - G345 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A331 - A344 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'C'
               Comment: ' // Basepair U332 - C343 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U333 - A342 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 14
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right 14
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right 13
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right 12
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   9  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  10  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  11   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_58126.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.2359
  -11.4192

Timestamp 18-Jul-2025 22:48:19
pMakeSCFGModels: Making JAR3D model for motif group IL_58350.1, number 234 of 411
pMakeNodes starting loop:     a=2NZ4|1|Q|G|119 B=2NZ4|1|Q|C|102
  2 Basepair   119  102 GC cWW 
No need to probe because of interaction between a=2NZ4|1|Q|G|120 B=2NZ4|1|Q|U|101
  3 Basepair   120  101 GU bif 
No need to probe because of interaction between a=2NZ4|1|Q|A|121 B=2NZ4|1|Q|A|100
  4 Basepair   121  100 AA tWH 
No need to probe because of interaction between a=2NZ4|1|Q|C|122 B=2NZ4|1|Q|A|99
  5 Basepair   122   99 CA tWH 
pMakeNodes probe for inserts:  a=2NZ4|1|Q|A|123 B=2NZ4|1|Q|A|98
    Insertion on left  2NZ4|1|Q|A|123
    Insertion on left  2NZ4|1|Q|A|124
    Insertion on left  2NZ4|1|Q|A|125
    Insertion on right 2NZ4|1|Q|A|98
pMakeNodesProbeForInsertions:  a 2NZ4|1|Q|G|126 interacts with 2NZ4|1|Q|U|96
pMakeNodesProbeForInsertions:  B 2NZ4|1|Q|U|96 interacts with 2NZ4|1|Q|G|126
pMakeNodesProbeForInsertions:  B 2NZ4|1|Q|U|96 interacts with 2NZ4|1|Q|G|126
pMakeNodes probed for insert:  a=2NZ4|1|Q|G|126 B=2NZ4|1|Q|U|96
  6 Basepair   126   96 GU cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 11
pMakeMotifModelFromSSF:   6  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   7   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2NZ4|1|Q|A|100
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2NZ4|1|Q|U|101
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2NZ4|1|Q|C|102
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 2NZ4|1|Q|A|121
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G119 - C102 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G120 - U101 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A121 - A100 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAAA'
           RightLetter: 'AA'
               Comment: ' // Basepair C122 - A99 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2NZ4|1|Q|A|100'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2NZ4|1|Q|U|101'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2NZ4|1|Q|C|102'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 2NZ4|1|Q|A|121'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G126 - U96 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 11
pMakeMotifModelFromSSF:   6     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   8     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  10     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  11   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  12     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  13   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  15   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a hairpin at node 15

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_58350.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2231

Timestamp 18-Jul-2025 22:48:20
pMakeSCFGModels: Making JAR3D model for motif group IL_58960.1, number 235 of 411
pMakeNodes starting loop:     a=4M4O|1|B|U|15 B=4M4O|1|B|A|45
  2 Basepair    15   45 UA cWW 
pMakeNodes probe for inserts:  a=4M4O|1|B|A|16 B=4M4O|1|B|C|44
    Insertion on left  4M4O|1|B|A|16
    Insertion on left  4M4O|1|B|A|17
pMakeNodesProbeForInsertions:  a 4M4O|1|B|A|18 interacts with 4M4O|1|B|U|22
pMakeNodesProbeForInsertions:  B 4M4O|1|B|C|44 interacts with 4M4O|1|B|G|23
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4M4O|1|B|C|44 interacts with 4M4O|1|B|G|23
pMakeNodes probed for insert:  a=4M4O|1|B|A|18 B=4M4O|1|B|C|44
pMakeNodes making a cluster near strand break a=4M4O|1|B|A|18 B=4M4O|1|B|C|44
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 9 and then 10 to 10
aa is 9 bb is 10
  3 Cluster   4M4O|1|B|A|18:4M4O|1|B|G|23 4M4O|1|B|C|44:4M4O|1|B|C|44
    LR Inter  4M4O|1|B|G|23 4M4O|1|B|C|44 cWW 
    LL Inter  4M4O|1|B|A|18 4M4O|1|B|U|22 tWW 
    Left  strand conserved insertion 4M4O|1|B|G|19 at position 2
    Left  strand conserved insertion 4M4O|1|B|A|20 at position 3
    Left  strand conserved insertion 4M4O|1|B|G|21 at position 4
pMakeNodesCluster a=10 B=9 at the end
pMakeNodesCluster a=10 B=9 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  4  5  6  7  8  9 Right 10
pMakeMotifModelFromSSF:   4   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4M4O|1|B|A|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4M4O|1|B|A|17
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UAA'
           RightLetter: 'A'
               Comment: ' // Basepair U15 - A45 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4M4O|1|B|A|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 1

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4M4O|1|B|A|17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [4 5 6 7 8 9]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGAGUG'
           RightLetter: 'C'
               Comment: ' // Cluster node 4M4O|1|B|A|18:4M4O|1|B|G|23 and 4M4O|1|B|C|44:4M4O|1|B|C|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7   Cluster Left  4  5  6  7  8  9 Right 10
pMakeMotifModelFromSSF:   8   Initial Left 10 Right  9
pMakeMotifModelFromSSF:   9   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 9
pUpdateModelWithSSF: IL_58960.1 allow insertions from initial node 8?
ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_58960.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1288
   -6.1288
   -7.2086

Timestamp 18-Jul-2025 22:48:20
pMakeSCFGModels: Making JAR3D model for motif group IL_59049.1, number 236 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|G|751 B=8P9A|1|sR|C|798
  2 Basepair   751  798 GC cWW 
No need to probe because of interaction between a=8P9A|1|sR|A|752 B=8P9A|1|sR|G|797
  3 Basepair   752  797 AG cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|A|753 B=8P9A|1|sR|A|796
    Insertion on right 8P9A|1|sR|A|796
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|A|753 interacts with 8P9A|1|sR|U|794
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|794 interacts with 8P9A|1|sR|A|753
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|794 interacts with 8P9A|1|sR|A|753
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|sR|A|753 B=8P9A|1|sR|U|794
  4 Basepair   753  794 AU cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|A|754 B=8P9A|1|sR|A|793
    Insertion on left  8P9A|1|sR|A|754
    Insertion on left  8P9A|1|sR|A|755
    Insertion on left  8P9A|1|sR|A|756
    Insertion on left  8P9A|1|sR|A|757
    Insertion on left  8P9A|1|sR|U|758
    Insertion on right 8P9A|1|sR|A|793
    Insertion on right 8P9A|1|sR|U|792
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|U|759 interacts with 8P9A|1|sR|A|791
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|A|791 interacts with 8P9A|1|sR|U|759
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|A|791 interacts with 8P9A|1|sR|U|759
pMakeNodes probed for insert:  a=8P9A|1|sR|U|759 B=8P9A|1|sR|A|791
  5 Basepair   759  791 UA cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 15
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   5  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   6   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|U|795
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|A|754
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|A|755
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|A|756
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|A|757
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|U|758
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|A|793
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|U|792
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G751 - C798 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'AG'
               Comment: ' // Basepair A752 - G797 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|U|795'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAAAAU'
           RightLetter: 'UAU'
               Comment: ' // Basepair A753 - U794 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
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            RightIndex: 12
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       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|A|754'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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                     P: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
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        leftLengthDist: [0 1]
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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               Comment: ' // Fixed node on left for 8P9A|1|sR|A|755'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
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        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
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        leftLengthDist: [0 1]
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
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               Comment: ' // Fixed node on left for 8P9A|1|sR|A|756'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
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                     P: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 14
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        leftLengthDist: [0 1]
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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               Comment: ' // Fixed node on left for 8P9A|1|sR|A|757'
              NumLoops: []
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                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
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             Insertion: []
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        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
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             Insertion: []
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        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|U|758'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|A|793'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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                     P: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|U|792'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U759 - A791 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 25
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 15
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 14
pMakeMotifModelFromSSF:   5   Initial Left  3 Right 13
pMakeMotifModelFromSSF:   6  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 12
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 12
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 12
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 12
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  19     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  20   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  21  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  22   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Found a hairpin at node 22

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_59049.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.8977
   -8.8977

Timestamp 18-Jul-2025 22:48:20
pMakeSCFGModels: Making JAR3D model for motif group IL_59258.1, number 237 of 411
pMakeNodes starting loop:     a=5XTM|1|D|G|8 B=5XTM|1|D|C|39
  2 Basepair     8   39 GC cWW 
No need to probe because of interaction between a=5XTM|1|D|A|9 B=5XTM|1|D|C|38
  3 Basepair     9   38 AC cWW 
pMakeNodes probe for inserts:  a=5XTM|1|D|U|10 B=5XTM|1|D|A|37
    Insertion on left  5XTM|1|D|U|10
    Insertion on left  5XTM|1|D|G|11
    Insertion on left  5XTM|1|D|A|12
    Insertion on right 5XTM|1|D|A|37
pMakeNodesProbeForInsertions:  a 5XTM|1|D|A|13 interacts with 5XTM|1|D|A|36
pMakeNodesProbeForInsertions:  B 5XTM|1|D|A|36 interacts with 5XTM|1|D|A|13
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5XTM|1|D|A|36 interacts with 5XTM|1|D|A|13
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5XTM|1|D|A|13 B=5XTM|1|D|A|36
  4 Basepair    13   36 AA cWW 
No need to probe because of interaction between a=5XTM|1|D|A|14 B=5XTM|1|D|U|35
  5 Basepair    14   35 AU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5XTM|1|D|U|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5XTM|1|D|G|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5XTM|1|D|A|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5XTM|1|D|A|37
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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                  lpar: []
                  rpar: []
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Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G8 - C39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AUGA'
           RightLetter: 'AC'
               Comment: ' // Basepair A9 - C38 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5XTM|1|D|U|10'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5XTM|1|D|G|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5XTM|1|D|A|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                  lpar: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5XTM|1|D|A|37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                IBases: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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                  lpar: []
                  rpar: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A13 - A36 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A14 - U35 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  11   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  13  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  14   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_59258.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.5992

Timestamp 18-Jul-2025 22:48:21
pMakeSCFGModels: Making JAR3D model for motif group IL_59302.1, number 238 of 411
pMakeNodes starting loop:     a=4V9F|1|0|U|548 B=4V9F|1|0|A|608
  2 Basepair   548  608 UA cWW 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|549 B=4V9F|1|0|G|607
    Insertion on left  4V9F|1|0|A|549
    Insertion on left  4V9F|1|0|C|550
    Insertion on left  4V9F|1|0|A|551
    Insertion on left  4V9F|1|0|A|552
    Insertion on right 4V9F|1|0|G|607
pMakeNodesProbeForInsertions:  a 4V9F|1|0|G|553 interacts with 4V9F|1|0|C|606
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|606 interacts with 4V9F|1|0|G|553
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|606 interacts with 4V9F|1|0|G|553
pMakeNodes probed for insert:  a=4V9F|1|0|G|553 B=4V9F|1|0|C|606
  3 Basepair   553  606 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|549
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|C|550
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|551
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|552
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4V9F|1|0|G|607
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UACAA'
           RightLetter: 'GA'
               Comment: ' // Basepair U548 - A608 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|A|549'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|C|550'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                IBases: []
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                  rpar: []
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                  lpar: []
                  rpar: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|A|551'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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               subtype: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|A|552'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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               subtype: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4V9F|1|0|G|607'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G553 - C606 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_59302.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4258
   -6.4258

Timestamp 18-Jul-2025 22:48:21
pMakeSCFGModels: Making JAR3D model for motif group IL_59724.1, number 239 of 411
pMakeNodes starting loop:     a=4V9F|1|0|C|355 B=4V9F|1|0|G|296
  2 Basepair   355  296 CG cWW 
No need to probe because of interaction between a=4V9F|1|0|C|356 B=4V9F|1|0|C|295
  3 Basepair   356  295 CC bif 
No need to probe because of interaction between a=4V9F|1|0|A|357 B=4V9F|1|0|C|294
  4 Basepair   357  294 AC tHH 
pMakeNodes probe for inserts:  a=4V9F|1|0|G|358 B=4V9F|1|0|A|293
pMakeNodesProbeForInsertions:  a 4V9F|1|0|G|358 interacts with 4V9F|1|0|U|359
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|293 interacts with 4V9F|1|0|U|359
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4V9F|1|0|A|293 interacts with 4V9F|1|0|U|359
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4V9F|1|0|G|358 B=4V9F|1|0|A|293
pMakeNodes making a cluster near strand break a=4V9F|1|0|G|358 B=4V9F|1|0|A|293
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 12 to 12
aa is 5 bb is 12
  5 Cluster   4V9F|1|0|G|358:4V9F|1|0|U|359 4V9F|1|0|A|293:4V9F|1|0|A|293
    LR Inter  4V9F|1|0|U|359 4V9F|1|0|A|293 tWH 
    LL Inter  4V9F|1|0|G|358 4V9F|1|0|U|359 cSH 
pMakeNodesCluster a=6 B=11 at the end
pMakeNodesCluster a=6 B=11 at the end
No need to probe because of interaction between a=4V9F|1|0|A|360 B=4V9F|1|0|G|292
  6 Basepair   360  292 AG tHS 
No need to probe because of interaction between a=4V9F|1|0|C|361 B=4V9F|1|0|C|291
  7 Basepair   361  291 CC bif 
No need to probe because of interaction between a=4V9F|1|0|G|362 B=4V9F|1|0|C|290
  8 Basepair   362  290 GC cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 12
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   9   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C355 - G296 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C356 - C295 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A357 - C294 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [4 5]
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 4V9F|1|0|G|358:4V9F|1|0|U|359 and 4V9F|1|0|A|293:4V9F|1|0|A|293'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A360 - G292 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C361 - C291 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G362 - C290 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  6 Right 11
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_59724.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.2989

Timestamp 18-Jul-2025 22:48:22
pMakeSCFGModels: Making JAR3D model for motif group IL_59877.1, number 240 of 411
pMakeNodes starting loop:     a=1XJR|1|A|G|28 B=1XJR|1|A|C|20
pMakeNodes making a cluster near strand break a=1XJR|1|A|G|28 B=1XJR|1|A|C|20
pMakeNodesCluster: amax is 3 bmin is 4, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 3 and then 4 to 5
aa is 3 bb is 4
  2 Cluster   1XJR|1|A|G|28:1XJR|1|A|C|31 1XJR|1|A|G|19:1XJR|1|A|C|20
    LR Inter  1XJR|1|A|C|31 1XJR|1|A|G|19 cWW 
    LR Inter  1XJR|1|A|G|28 1XJR|1|A|C|20 cWW 
    LL Inter  1XJR|1|A|G|28 1XJR|1|A|C|31 cSS 
    Left  strand conserved insertion 1XJR|1|A|A|29 at position 2
pMakeNodesCluster a=4 B=3 at the end
pMakeNodesCluster a=4 B=3 at the end
  3 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  4  5
pMakeMotifModelFromSSF:   3   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3]
            RightIndex: [4 5]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAC'
           RightLetter: 'GC'
               Comment: ' // Cluster node 1XJR|1|A|G|28:1XJR|1|A|C|31 and 1XJR|1|A|G|19:1XJR|1|A|C|20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.0629

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  4  5
pMakeMotifModelFromSSF:   3   Initial Left  4 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 4
pUpdateModelWithSSF: IL_59877.1 allow insertions from initial node 3?
ans =

    0.9739    0.0249    0.0012


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9739    0.0249    0.0012


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_59877.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.8610
   -3.6873

Timestamp 18-Jul-2025 22:48:22
pMakeSCFGModels: Making JAR3D model for motif group IL_60448.1, number 241 of 411
pMakeNodes starting loop:     a=3NPQ|1|A|G|7 B=3NPQ|1|A|C|32
  2 Basepair     7   32 GC cWW 
pMakeNodes probe for inserts:  a=3NPQ|1|A|G|8 B=3NPQ|1|A|G|31
    Insertion on left  3NPQ|1|A|G|8
    Insertion on left  3NPQ|1|A|A|9
    Insertion on left  3NPQ|1|A|G|10
    Insertion on left  3NPQ|1|A|C|11
    Insertion on left  3NPQ|1|A|G|12
    Insertion on left  3NPQ|1|A|C|13
pMakeNodesProbeForInsertions:  a 3NPQ|1|A|U|14 interacts with 3NPQ|1|A|A|29
pMakeNodesProbeForInsertions:  B 3NPQ|1|A|G|31 interacts with 3NPQ|1|A|C|16
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3NPQ|1|A|G|31 interacts with 3NPQ|1|A|C|16
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3NPQ|1|A|U|14 B=3NPQ|1|A|G|31
pMakeNodes making a cluster near strand break a=3NPQ|1|A|U|14 B=3NPQ|1|A|G|31
pMakeNodesCluster: amax is 13 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 8 to 11 and then 16 to 19
aa is 11 bb is 16
  3 Cluster   3NPQ|1|A|U|14:3NPQ|1|A|A|17 3NPQ|1|A|C|28:3NPQ|1|A|G|31
    LR Inter  3NPQ|1|A|C|16 3NPQ|1|A|C|28 tHS 
    LR Inter  3NPQ|1|A|A|17 3NPQ|1|A|C|28 tHS 
    LR Inter  3NPQ|1|A|U|14 3NPQ|1|A|A|29 tWH 
    LR Inter  3NPQ|1|A|C|16 3NPQ|1|A|G|31 cWW 
    Left  strand conserved insertion 3NPQ|1|A|G|15 at position 2
    Right strand conserved insertion 3NPQ|1|A|G|30 at position 3
pMakeNodesCluster a=12 B=15 at the end
pMakeNodesCluster a=12 B=15 at the end
No need to probe because of interaction between a=3NPQ|1|A|A|18 B=3NPQ|1|A|C|27
  4 Basepair    18   27 AC bif 
No need to probe because of interaction between a=3NPQ|1|A|G|19 B=3NPQ|1|A|C|26
  5 Basepair    19   26 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 20
pMakeMotifModelFromSSF:   3   Cluster Left  8  9 10 11 Right 16 17 18 19
pMakeMotifModelFromSSF:   4  Basepair Left 12 Right 15
pMakeMotifModelFromSSF:   5  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:   6   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|G|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|A|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|G|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|C|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|G|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3NPQ|1|A|C|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 20
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [20×20 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGAGCGC'
           RightLetter: 'C'
               Comment: ' // Basepair G7 - C32 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|G|8'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: 3
              NormCons: 0.0652

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|A|9'
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|G|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 14
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|C|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|G|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3NPQ|1|A|C|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 16
             LeftIndex: [8 9 10 11]
            RightIndex: [16 17 18 19]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGCA'
           RightLetter: 'CAGG'
               Comment: ' // Cluster node 3NPQ|1|A|U|14:3NPQ|1|A|A|17 and 3NPQ|1|A|C|28:3NPQ|1|A|G|31'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: 3
              NormCons: 0.0652

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 12
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 12
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A18 - C27 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 19
             LeftIndex: 13
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G19 - C26 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 21
             LeftIndex: 14
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 14
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 20
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 19
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 19
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 19
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 19
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 19
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 19
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 19
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 19
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 19
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 19
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 19
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 19
pMakeMotifModelFromSSF:  15   Cluster Left  8  9 10 11 Right 16 17 18 19
pMakeMotifModelFromSSF:  16   Initial Left 12 Right 15
pMakeMotifModelFromSSF:  17  Basepair Left 12 Right 15
pMakeMotifModelFromSSF:  18  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  19   Hairpin Left 14 Right 13
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Found a hairpin at node 19

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_60448.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.0383

Timestamp 18-Jul-2025 22:48:22
pMakeSCFGModels: Making JAR3D model for motif group IL_60657.1, number 242 of 411
pMakeNodes starting loop:     a=4ZNP|1|A|C|12 B=4ZNP|1|A|G|37
  2 Basepair    12   37 CG cWW 
No need to probe because of interaction between a=4ZNP|1|A|U|13 B=4ZNP|1|A|U|36
  3 Basepair    13   36 UU cWW 
pMakeNodes probe for inserts:  a=4ZNP|1|A|G|14 B=4ZNP|1|A|G|35
    Insertion on left  4ZNP|1|A|G|14
    Insertion on left  4ZNP|1|A|G|15
    Insertion on left  4ZNP|1|A|C|16
    Insertion on left  4ZNP|1|A|G|17
    Insertion on left  4ZNP|1|A|G|18
    Insertion on left  4ZNP|1|A|A|19
    Insertion on left  4ZNP|1|A|U|20
    Insertion on left  4ZNP|1|A|U|21
    Insertion on left  4ZNP|1|A|A|22
    Insertion on right 4ZNP|1|A|G|35
pMakeNodesProbeForInsertions:  a 4ZNP|1|A|G|23 interacts with 4ZNP|1|A|C|34
pMakeNodesProbeForInsertions:  B 4ZNP|1|A|C|34 interacts with 4ZNP|1|A|G|23
pMakeNodesProbeForInsertions:  B 4ZNP|1|A|C|34 interacts with 4ZNP|1|A|G|23
pMakeNodes probed for insert:  a=4ZNP|1|A|G|23 B=4ZNP|1|A|C|34
  4 Basepair    23   34 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 15
pMakeMotifModelFromSSF:   4  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:   5   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4ZNP|1|A|G|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4ZNP|1|A|G|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4ZNP|1|A|C|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4ZNP|1|A|G|17
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4ZNP|1|A|G|18
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4ZNP|1|A|A|19
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4ZNP|1|A|U|20
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4ZNP|1|A|U|21
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4ZNP|1|A|A|22
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4ZNP|1|A|G|35
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C12 - G37 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-10 8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGGCGGAUUA'
           RightLetter: 'GU'
               Comment: ' // Basepair U13 - U36 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4ZNP|1|A|G|14'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4ZNP|1|A|G|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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      JunctionDeletion: []
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                  lpar: []
                  rpar: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4ZNP|1|A|C|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
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                  lpar: []
                  rpar: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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                  lpar: []
                  rpar: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4ZNP|1|A|G|17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
    InteractionComment: []
      JunctionDeletion: []
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                  lpar: []
                  rpar: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4ZNP|1|A|G|18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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                  rpar: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
    InteractionComment: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4ZNP|1|A|A|19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                IBases: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4ZNP|1|A|U|20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 10
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4ZNP|1|A|U|21'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4ZNP|1|A|A|22'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             LeftIndex: 12
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 23
             LeftIndex: 12
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4ZNP|1|A|G|35'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 24
             LeftIndex: 12
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 25
             LeftIndex: 12
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G23 - C34 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 27
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 15
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 14
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 14
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 14
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 14
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 14
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 14
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 14
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 14
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 14
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 14
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 14
pMakeMotifModelFromSSF:  16     Fixed Left  9 Right 14
pMakeMotifModelFromSSF:  17   Initial Left 10 Right 14
pMakeMotifModelFromSSF:  18     Fixed Left 10 Right 14
pMakeMotifModelFromSSF:  19   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  20     Fixed Left 11 Right 14
pMakeMotifModelFromSSF:  21   Initial Left 12 Right 14
pMakeMotifModelFromSSF:  22     Fixed Left 12 Right 14
pMakeMotifModelFromSSF:  23   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  24  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  25   Hairpin Left 13 Right 12
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Found a hairpin at node 25

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_60657.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.5146

Timestamp 18-Jul-2025 22:48:23
pMakeSCFGModels: Making JAR3D model for motif group IL_60797.1, number 243 of 411
pMakeNodes starting loop:     a=2P7E|1|C|G|19 B=2P7E|1|D|C|45
  2 Basepair    19   45 GC cWW 
No need to probe because of interaction between a=2P7E|1|C|A|20 B=2P7E|1|D|C|44
  3 Basepair    20   44 AC cWW 
No need to probe because of interaction between a=2P7E|1|C|G|21 B=2P7E|1|D|A|43
  4 Basepair    21   43 GA tSH 
No need to probe because of interaction between a=2P7E|1|C|A|22 B=2P7E|1|D|U|41
  5 Basepair    22   41 AU tHW 
No need to probe because of interaction between a=2P7E|1|C|A|23 B=2P7E|1|D|A|40
  6 Basepair    23   40 AA tHW 
No need to probe because of interaction between a=2P7E|1|C|A|24 B=2P7E|1|D|A|38
  7 Basepair    24   38 AA tWH 
pMakeNodes probe for inserts:  a=2P7E|1|C|C|25 B=2P7E|1|D|G|36
    Insertion on left  2P7E|1|C|C|25
pMakeNodesProbeForInsertions:  a 2P7E|1|C|A|26 interacts with 2P7E|1|D|G|36
pMakeNodesProbeForInsertions:  B 2P7E|1|D|G|36 interacts with 2P7E|1|C|A|26
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 2P7E|1|D|G|36 interacts with 2P7E|1|C|A|26
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=2P7E|1|C|A|26 B=2P7E|1|D|G|36
  8 Basepair    26   36 AG cWW 
No need to probe because of interaction between a=2P7E|1|C|C|27 B=2P7E|1|D|G|35
  9 Basepair    27   35 CG cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 15
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 14
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right 13
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right 12
pMakeMotifModelFromSSF:   8  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:   9  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  10   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2P7E|1|C|C|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [17×17 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G19 - C45 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A20 - C44 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G21 - A43 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A22 - U41 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A23 - A40 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AC'
           RightLetter: 'A'
               Comment: ' // Basepair A24 - A38 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2P7E|1|C|C|25'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A26 - G36 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C27 - G35 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 15
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 14
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right 13
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right 12
pMakeMotifModelFromSSF:   8     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:   9   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  11  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  12   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_60797.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.5598
  -11.6931
   -9.5598
  -10.4071

Timestamp 18-Jul-2025 22:48:24
pMakeSCFGModels: Making JAR3D model for motif group IL_61242.1, number 244 of 411
pMakeNodes starting loop:     a=4Z31|1|C|C|6 B=4Z31|1|D|G|10
  2 Basepair     6   10 CG cWW 
No need to probe because of interaction between a=4Z31|1|C|U|7 B=4Z31|1|D|U|9
  3 Basepair     7    9 UU cWW 
pMakeNodes probe for inserts:  a=4Z31|1|C|G|8 B=4Z31|1|D|G|8
    Insertion on left  4Z31|1|C|G|8
    Insertion on right 4Z31|1|D|G|8
pMakeNodesProbeForInsertions:  a 4Z31|1|C|U|9 interacts with 4Z31|1|D|U|7
pMakeNodesProbeForInsertions:  B 4Z31|1|D|U|7 interacts with 4Z31|1|C|U|9
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4Z31|1|D|U|7 interacts with 4Z31|1|C|U|9
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4Z31|1|C|U|9 B=4Z31|1|D|U|7
  4 Basepair     9    7 UU cWW 
No need to probe because of interaction between a=4Z31|1|C|G|10 B=4Z31|1|D|C|6
  5 Basepair    10    6 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4Z31|1|C|G|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4Z31|1|D|G|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C6 - G10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UG'
           RightLetter: 'GU'
               Comment: ' // Basepair U7 - U9 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4Z31|1|C|G|8'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4Z31|1|D|G|8'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U9 - U7 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G10 - C6 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  10   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_61242.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.2390

Timestamp 18-Jul-2025 22:48:24
pMakeSCFGModels: Making JAR3D model for motif group IL_61249.1, number 245 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|U|1851 B=5J7L|1|DA|G|1891
  2 Basepair  1851 1891 UG cWW 
No need to probe because of interaction between a=5J7L|1|DA|U|1852 B=5J7L|1|DA|A|1890
  3 Basepair  1852 1890 UA tSH 
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|1853 B=5J7L|1|DA|A|1889
    Insertion on left  5J7L|1|DA|A|1853
    Insertion on right 5J7L|1|DA|A|1889
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|A|1854 interacts with 5J7L|1|DA|G|1888
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|1888 interacts with 5J7L|1|DA|A|1854
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|1888 interacts with 5J7L|1|DA|A|1854
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5J7L|1|DA|A|1854 B=5J7L|1|DA|G|1888
  4 Basepair  1854 1888 AG tHS 
No need to probe because of interaction between a=5J7L|1|DA|U|1855 B=5J7L|1|DA|C|1887
  5 Basepair  1855 1887 UC cWW 
No need to probe because of interaction between a=5J7L|1|DA|U|1856 B=5J7L|1|DA|U|1886
  6 Basepair  1856 1886 UU cWW 
No need to probe because of interaction between a=5J7L|1|DA|G|1857 B=5J7L|1|DA|A|1885
  7 Basepair  1857 1885 GA tSH 
No need to probe because of interaction between a=5J7L|1|DA|A|1858 B=5J7L|1|DA|G|1884
  8 Basepair  1858 1884 AG tHS 
No need to probe because of interaction between a=5J7L|1|DA|U|1859 B=5J7L|1|DA|U|1883
  9 Basepair  1859 1883 UU cWW 
No need to probe because of interaction between a=5J7L|1|DA|G|1860 B=5J7L|1|DA|U|1882
 10 Basepair  1860 1882 GU cWW 
 11 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 20
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 19
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right 17
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right 16
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right 15
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right 14
pMakeMotifModelFromSSF:   8  Basepair Left  8 Right 13
pMakeMotifModelFromSSF:   9  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  10  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  11   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|1853
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|A|1889
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 20
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [20×20 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U1851 - G1891 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: 'AA'
               Comment: ' // Basepair U1852 - A1890 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|1853'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|A|1889'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1854 - G1888 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'C'
               Comment: ' // Basepair U1855 - C1887 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U1856 - U1886 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1857 - A1885 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1858 - G1884 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U1859 - U1883 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1860 - U1882 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 20
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 20
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 19
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 18
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 18
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 18
pMakeMotifModelFromSSF:   7   Initial Left  4 Right 17
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right 17
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right 16
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right 15
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right 14
pMakeMotifModelFromSSF:  12  Basepair Left  8 Right 13
pMakeMotifModelFromSSF:  13  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:  14  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  15   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a hairpin at node 15

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_61249.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.8617

Timestamp 18-Jul-2025 22:48:24
pMakeSCFGModels: Making JAR3D model for motif group IL_61258.15, number 246 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|C|994 B=9DFE|1|1A|G|1160
  2 Basepair   994 1160 CG cWW 
pMakeNodes probe for inserts:  a=9DFE|1|1A|C|995 B=9DFE|1|1A|U|1159
    Insertion on left  9DFE|1|1A|C|995
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|A|996 interacts with 9DFE|1|1A|U|1159
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|U|1159 interacts with 9DFE|1|1A|A|996
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|U|1159 interacts with 9DFE|1|1A|A|996
pMakeNodes probed for insert:  a=9DFE|1|1A|A|996 B=9DFE|1|1A|U|1159
  3 Basepair   996 1159 AU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|C|995
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CC'
           RightLetter: 'G'
               Comment: ' // Basepair C994 - G1160 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|C|995'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A996 - U1159 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_61258.15_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.4083
   -3.4083
   -3.1941
   -3.4083
   -3.3629
   -2.8255
   -2.5432
   -2.7761
   -2.5432
   -2.8255
   -3.0584
   -2.7761
   -2.5432
   -2.7761
   -2.8255
   -2.7761
   -2.5432
   -2.7761
   -3.3629
   -2.7761
   -2.8255
   -3.3629
   -2.8255
   -2.5432
   -3.1941
   -3.0265
   -2.5432
   -2.5432
   -2.7761
   -2.8255
   -3.1941
   -2.5432
   -2.5432
   -2.5432
   -2.5432
   -3.1941
   -3.0397
   -3.5231
   -3.0265
   -2.5432
   -5.1363

Timestamp 18-Jul-2025 22:48:25
pMakeSCFGModels: Making JAR3D model for motif group IL_61286.1, number 247 of 411
pMakeNodes starting loop:     a=3IGI|1|A|C|296 B=3IGI|1|A|G|321
  2 Basepair   296  321 CG cWW 
pMakeNodes probe for inserts:  a=3IGI|1|A|A|297 B=3IGI|1|A|G|320
    Insertion on left  3IGI|1|A|A|297
    Insertion on left  3IGI|1|A|U|298
    Insertion on right 3IGI|1|A|G|320
pMakeNodesProbeForInsertions:  a 3IGI|1|A|A|299 interacts with 3IGI|1|A|A|319
pMakeNodesProbeForInsertions:  B 3IGI|1|A|A|319 interacts with 3IGI|1|A|A|299
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3IGI|1|A|A|319 interacts with 3IGI|1|A|A|299
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3IGI|1|A|A|299 B=3IGI|1|A|A|319
  3 Basepair   299  319 AA tHH 
pMakeNodes probe for inserts:  a=3IGI|1|A|G|300 B=3IGI|1|A|A|318
    Insertion on left  3IGI|1|A|G|300
pMakeNodesProbeForInsertions:  a 3IGI|1|A|U|301 interacts with 3IGI|1|A|A|318
pMakeNodesProbeForInsertions:  B 3IGI|1|A|A|318 interacts with 3IGI|1|A|U|301
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3IGI|1|A|A|318 interacts with 3IGI|1|A|U|301
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3IGI|1|A|U|301 B=3IGI|1|A|A|318
  4 Basepair   301  318 UA tWH 
No need to probe because of interaction between a=3IGI|1|A|A|302 B=3IGI|1|A|G|317
  5 Basepair   302  317 AG tHS 
No need to probe because of interaction between a=3IGI|1|A|C|303 B=3IGI|1|A|G|316
  6 Basepair   303  316 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   7   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|A|297
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|U|298
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3IGI|1|A|G|320
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|G|300
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAU'
           RightLetter: 'GG'
               Comment: ' // Basepair C296 - G321 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IGI|1|A|A|297'
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IGI|1|A|U|298'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3IGI|1|A|G|320'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: 'A'
               Comment: ' // Basepair A299 - A319 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IGI|1|A|G|300'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U301 - A318 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A302 - G317 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C303 - G316 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 13
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 13
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 13
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 13
pMakeMotifModelFromSSF:   8   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right 12
pMakeMotifModelFromSSF:  10     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:  13  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  14  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  15   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a hairpin at node 15

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_61286.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.6353

Timestamp 18-Jul-2025 22:48:26
pMakeSCFGModels: Making JAR3D model for motif group IL_61299.4, number 248 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|U|58 B=8P9A|1|sR|G|89
  2 Basepair    58   89 UG cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|C|59 B=8P9A|1|sR|U|88
    Insertion on right 8P9A|1|sR|U|88
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|C|59 interacts with 8P9A|1|sR|G|63
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|C|87 interacts with 8P9A|1|sR|G|63
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|C|87 interacts with 8P9A|1|sR|G|63
pMakeNodes probed for insert:  a=8P9A|1|sR|C|59 B=8P9A|1|sR|C|87
pMakeNodes making a cluster near strand break a=8P9A|1|sR|C|59 B=8P9A|1|sR|C|87
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 6 and then 7 to 7
aa is 6 bb is 7
  3 Cluster   8P9A|1|sR|C|59:8P9A|1|sR|G|63 8P9A|1|sR|C|87:8P9A|1|sR|C|87
    LR Inter  8P9A|1|sR|G|63 8P9A|1|sR|C|87 cWW 
    LL Inter  8P9A|1|sR|C|59 8P9A|1|sR|G|63 cWH 
    Left  strand conserved insertion 8P9A|1|sR|U|60 at position 2
    Left  strand conserved insertion 8P9A|1|sR|A|61 at position 3
    Left  strand conserved insertion 8P9A|1|sR|A|62 at position 4
pMakeNodesCluster a=7 B=6 at the end
pMakeNodesCluster a=7 B=6 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|U|88
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'UG'
               Comment: ' // Basepair U58 - G89 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|U|88'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 0.2500

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [2 3 4 5 6]
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUAAG'
           RightLetter: 'C'
               Comment: ' // Cluster node 8P9A|1|sR|C|59:8P9A|1|sR|G|63 and 8P9A|1|sR|C|87:8P9A|1|sR|C|87'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 0.2500

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  7
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  7 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 7
pUpdateModelWithSSF: IL_61299.4 allow insertions from initial node 6?
ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_61299.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.9841
   -5.9841
   -7.6616

Timestamp 18-Jul-2025 22:48:26
pMakeSCFGModels: Making JAR3D model for motif group IL_61341.1, number 249 of 411
pMakeNodes starting loop:     a=3OXE|1|A|C|31 B=3OXE|1|A|G|72
  2 Basepair    31   72 CG cWW 
No need to probe because of interaction between a=3OXE|1|A|G|32 B=3OXE|1|A|A|71
  3 Basepair    32   71 GA cHW 
No need to probe because of interaction between a=3OXE|1|A|G|35 B=3OXE|1|A|C|70
  4 Basepair    35   70 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C31 - G72 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G32 - A71 cHW '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G35 - C70 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_61341.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.5419
   -6.9381

Timestamp 18-Jul-2025 22:48:26
pMakeSCFGModels: Making JAR3D model for motif group IL_61438.4, number 250 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|C|1764 B=8P9A|1|sR|G|1638
  2 Basepair  1764 1638 CG cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|A|1765 B=8P9A|1|sR|C|1636
    Insertion on left  8P9A|1|sR|A|1765
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|G|1767 interacts with 8P9A|1|sR|C|1636
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|C|1636 interacts with 8P9A|1|sR|G|1767
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|C|1636 interacts with 8P9A|1|sR|G|1767
pMakeNodes probed for insert:  a=8P9A|1|sR|G|1767 B=8P9A|1|sR|C|1636
  3 Basepair  1767 1636 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|C|1637
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: 'G'
               Comment: ' // Basepair C1764 - G1638 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|C|1637'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1767 - C1636 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_61438.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.7299
   -2.7299
   -2.7299
   -2.7299

Timestamp 18-Jul-2025 22:48:27
pMakeSCFGModels: Making JAR3D model for motif group IL_61440.1, number 251 of 411
pMakeNodes starting loop:     a=4UYK|1|R|C|86 B=4UYK|1|R|G|115
  2 Basepair    86  115 CG cWW 
No need to probe because of interaction between a=4UYK|1|R|G|87 B=4UYK|1|R|A|114
  3 Basepair    87  114 GA tSH 
No need to probe because of interaction between a=4UYK|1|R|A|88 B=4UYK|1|R|G|113
  4 Basepair    88  113 AG tHS 
No need to probe because of interaction between a=4UYK|1|R|A|89 B=4UYK|1|R|G|112
  5 Basepair    89  112 AG tWS 
No need to probe because of interaction between a=4UYK|1|R|G|90 B=4UYK|1|R|U|111
  6 Basepair    90  111 GU cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C86 - G115 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G87 - A114 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A88 - G113 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A89 - G112 tWS '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G90 - U111 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 1 of 1, pair 4,7 for nucleotide 4 (A) making self BPh with edge 1
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_61440.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.9696

Timestamp 18-Jul-2025 22:48:27
pMakeSCFGModels: Making JAR3D model for motif group IL_61476.2, number 252 of 411
pMakeNodes starting loop:     a=4V9F|1|0|C|2351 B=4V9F|1|0|G|2333
  2 Basepair  2351 2333 CG cWW 
No need to probe because of interaction between a=4V9F|1|0|G|2352 B=4V9F|1|0|A|2332
  3 Basepair  2352 2332 GA tSH 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|2353 B=4V9F|1|0|C|2331
    Insertion on left  4V9F|1|0|A|2353
    Insertion on left  4V9F|1|0|A|2354
pMakeNodesProbeForInsertions:  a 4V9F|1|0|G|2355 interacts with 4V9F|1|0|C|2331
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|2331 interacts with 4V9F|1|0|G|2355
pMakeNodesProbeForInsertions:  B 4V9F|1|0|C|2331 interacts with 4V9F|1|0|G|2355
pMakeNodes probed for insert:  a=4V9F|1|0|G|2355 B=4V9F|1|0|C|2331
  4 Basepair  2355 2331 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|G|2333
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|C|2351
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2351 - G2333 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAA'
           RightLetter: 'A'
               Comment: ' // Basepair G2352 - A2332 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|G|2333'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|C|2351'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2355 - C2331 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_61476.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1278
   -5.6170
   -5.9845
   -5.0301
   -5.0301
   -5.1249
   -7.3225

Timestamp 18-Jul-2025 22:48:27
pMakeSCFGModels: Making JAR3D model for motif group IL_62012.1, number 253 of 411
pMakeNodes starting loop:     a=2O3Y|1|B|A|38 B=2O3Y|1|A|U|10
  2 Basepair    38   10 AU cWW 
No need to probe because of interaction between a=2O3Y|1|B|A|39 B=2O3Y|1|A|C|9
  3 Basepair    39    9 AC cWW 
pMakeNodes probe for inserts:  a=2O3Y|1|B|A|40 B=2O3Y|1|A|G|8
    Insertion on left  2O3Y|1|B|A|40
    Insertion on left  2O3Y|1|B|A|41
    Insertion on right 2O3Y|1|A|G|8
pMakeNodesProbeForInsertions:  a 2O3Y|1|B|G|42 interacts with 2O3Y|1|A|C|7
pMakeNodesProbeForInsertions:  B 2O3Y|1|A|C|7 interacts with 2O3Y|1|B|G|42
pMakeNodesProbeForInsertions:  B 2O3Y|1|A|C|7 interacts with 2O3Y|1|B|G|42
pMakeNodes probed for insert:  a=2O3Y|1|B|G|42 B=2O3Y|1|A|C|7
  4 Basepair    42    7 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2O3Y|1|A|C|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2O3Y|1|A|U|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 2O3Y|1|B|A|40
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A38 - U10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAA'
           RightLetter: 'GC'
               Comment: ' // Basepair A39 - C9 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2O3Y|1|A|C|9'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2O3Y|1|A|U|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 2O3Y|1|B|A|40'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G42 - C7 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_62012.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3787

Timestamp 18-Jul-2025 22:48:28
pMakeSCFGModels: Making JAR3D model for motif group IL_62654.1, number 254 of 411
pMakeNodes starting loop:     a=4V9F|1|0|C|1570 B=4V9F|1|0|G|1627
  2 Basepair  1570 1627 CG cWW 
No need to probe because of interaction between a=4V9F|1|0|G|1571 B=4V9F|1|0|A|1626
  3 Basepair  1571 1626 GA tSH 
No need to probe because of interaction between a=4V9F|1|0|A|1572 B=4V9F|1|0|A|1624
  4 Basepair  1572 1624 AA tHH 
No need to probe because of interaction between a=4V9F|1|0|A|1573 B=4V9F|1|0|C|1623
  5 Basepair  1573 1623 AC tHS 
No need to probe because of interaction between a=4V9F|1|0|C|1574 B=4V9F|1|0|G|1622
  6 Basepair  1574 1622 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1570 - G1627 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1571 - A1626 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A1572 - A1624 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A1573 - C1623 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1574 - G1622 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_62654.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3930

Timestamp 18-Jul-2025 22:48:28
pMakeSCFGModels: Making JAR3D model for motif group IL_63519.1, number 255 of 411
pMakeNodes starting loop:     a=8D28|1|B|G|4 B=8D28|1|B|C|30
  2 Basepair     4   30 GC cWW 
No need to probe because of interaction between a=8D28|1|B|A|5 B=8D28|1|B|G|29
  3 Basepair     5   29 AG cWW 
No need to probe because of interaction between a=8D28|1|B|U|6 B=8D28|1|B|A|28
  4 Basepair     6   28 UA tSH 
pMakeNodes probe for inserts:  a=8D28|1|B|A|7 B=8D28|1|B|G|26
pMakeNodesProbeForInsertions:  a 8D28|1|B|A|7 interacts with 8D28|1|B|C|8
pMakeNodesProbeForInsertions:  B 8D28|1|B|G|26 interacts with 8D28|1|B|C|8
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8D28|1|B|G|26 interacts with 8D28|1|B|C|8
pMakeNodes probed for insert:  a=8D28|1|B|A|7 B=8D28|1|B|G|26
pMakeNodes making a cluster near strand break a=8D28|1|B|A|7 B=8D28|1|B|G|26
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 6 to 6
aa is 5 bb is 6
  5 Cluster   8D28|1|B|A|7:8D28|1|B|C|8 8D28|1|B|G|26:8D28|1|B|G|26
    LR Inter  8D28|1|B|C|8 8D28|1|B|G|26 cWW 
    LL Inter  8D28|1|B|A|7 8D28|1|B|C|8 cSH 
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G4 - C30 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A5 - G29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U6 - A28 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [4 5]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AC'
           RightLetter: 'G'
               Comment: ' // Cluster node 8D28|1|B|A|7:8D28|1|B|C|8 and 8D28|1|B|G|26:8D28|1|B|G|26'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2506

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   5   Cluster Left  4  5 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pUpdateModelWithSSF: IL_63519.1 allow insertions from initial node 6?
ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_63519.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3177
   -6.3177

Timestamp 18-Jul-2025 22:48:28
pMakeSCFGModels: Making JAR3D model for motif group IL_63596.11, number 256 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|U|2680 B=5J7L|1|DA|A|2727
pMakeNodes making a cluster near strand break a=5J7L|1|DA|U|2680 B=5J7L|1|DA|A|2727
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 6 to 7
aa is 5 bb is 6
  2 Cluster   5J7L|1|DA|U|2680:5J7L|1|DA|U|2684 5J7L|1|DA|A|2725:5J7L|1|DA|A|2727
    LR Inter  5J7L|1|DA|C|2681 5J7L|1|DA|A|2725 tWH 
    LR Inter  5J7L|1|DA|U|2684 5J7L|1|DA|A|2725 cWW 
    LR Inter  5J7L|1|DA|U|2680 5J7L|1|DA|A|2727 cWW 
    LR Inter  5J7L|1|DA|C|2683 5J7L|1|DA|A|2727 cWS 
    LL Inter  5J7L|1|DA|C|2681 5J7L|1|DA|C|2683 cSH 
    Left  strand conserved insertion 5J7L|1|DA|A|2682 at position 3
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  3 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  6  7
pMakeMotifModelFromSSF:   3   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: [6 7]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UCACU'
           RightLetter: 'AA'
               Comment: ' // Cluster node 5J7L|1|DA|U|2680:5J7L|1|DA|U|2684 and 5J7L|1|DA|A|2725:5J7L|1|DA|A|2727'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
          LeftNotInter: 3
         RightNotInter: [1×0 double]
              NormCons: 0.0047

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  6  7
pMakeMotifModelFromSSF:   3   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 4
pUpdateModelWithSSF: IL_63596.11 allow insertions from initial node 3?
ans =

    0.9972    0.0026    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9972    0.0026    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_63596.11_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4143
   -5.4776
   -3.4810
   -3.4810
   -3.4810
   -4.7265
   -7.1993
   -3.3559
   -3.3559
   -9.1433
   -5.0366
   -3.3559
   -9.1433
   -3.3559
   -4.7265
   -8.8282
   -6.4879
   -8.8255
   -8.8255

Timestamp 18-Jul-2025 22:48:29
pMakeSCFGModels: Making JAR3D model for motif group IL_63775.1, number 257 of 411
pMakeNodes starting loop:     a=5O6U|1|H|DC|3 B=5O6U|1|I|DG|25
pMakeNodes making a cluster near strand break a=5O6U|1|H|DC|3 B=5O6U|1|I|DG|25
pMakeNodesCluster: amax is 3 bmin is 4, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 5 to 5
aa is 2 bb is 5
  2 Cluster   5O6U|1|H|DC|3:5O6U|1|H|DC|4 5O6U|1|I|DG|25:5O6U|1|I|DG|25
    LR Inter  5O6U|1|H|DC|3 5O6U|1|I|DG|25 cWW 
    LR Inter  5O6U|1|H|DC|4 5O6U|1|I|DG|25 cWW 
pMakeNodesCluster a=3 B=4 at the end
pMakeNodesCluster a=3 B=4 at the end
No need to probe because of interaction between a=5O6U|1|H|DG|5 B=5O6U|1|I|DC|24
  3 Basepair     5   24 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CC'
           RightLetter: 'G'
               Comment: ' // Cluster node 5O6U|1|H|DC|3:5O6U|1|H|DC|4 and 5O6U|1|I|DG|25:5O6U|1|I|DG|25'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2500
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G5 - C24 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  5
pMakeMotifModelFromSSF:   3   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_63775.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.1649

Timestamp 18-Jul-2025 22:48:30
pMakeSCFGModels: Making JAR3D model for motif group IL_64048.1, number 258 of 411
pMakeNodes starting loop:     a=4MGN|1|A|C|37 B=4MGN|1|A|G|69
  2 Basepair    37   69 CG cWW 
pMakeNodes probe for inserts:  a=4MGN|1|A|G|39 B=4MGN|1|A|U|68
    Insertion on left  4MGN|1|A|G|39
    Insertion on left  4MGN|1|A|A|40
pMakeNodesProbeForInsertions:  a 4MGN|1|A|A|41 interacts with 4MGN|1|A|A|45
pMakeNodesProbeForInsertions:  B 4MGN|1|A|U|68 interacts with 4MGN|1|A|G|46
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4MGN|1|A|U|68 interacts with 4MGN|1|A|G|46
pMakeNodes probed for insert:  a=4MGN|1|A|A|41 B=4MGN|1|A|U|68
pMakeNodes making a cluster near strand break a=4MGN|1|A|A|41 B=4MGN|1|A|U|68
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 9 and then 10 to 10
aa is 9 bb is 10
  3 Cluster   4MGN|1|A|A|41:4MGN|1|A|G|46 4MGN|1|A|U|68:4MGN|1|A|U|68
    LR Inter  4MGN|1|A|G|46 4MGN|1|A|U|68 cWW 
    LL Inter  4MGN|1|A|A|41 4MGN|1|A|A|45 tWH 
    Left  strand conserved insertion 4MGN|1|A|G|42 at position 2
    Left  strand conserved insertion 4MGN|1|A|C|43 at position 3
    Left  strand conserved insertion 4MGN|1|A|G|44 at position 4
pMakeNodesCluster a=10 B=9 at the end
pMakeNodesCluster a=10 B=9 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  4  5  6  7  8  9 Right 10
pMakeMotifModelFromSSF:   4   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4MGN|1|A|C|38
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4MGN|1|A|G|39
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGA'
           RightLetter: 'G'
               Comment: ' // Basepair C37 - G69 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4MGN|1|A|C|38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 1

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4MGN|1|A|G|39'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [4 5 6 7 8 9]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGCGAG'
           RightLetter: 'U'
               Comment: ' // Cluster node 4MGN|1|A|A|41:4MGN|1|A|G|46 and 4MGN|1|A|U|68:4MGN|1|A|U|68'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7   Cluster Left  4  5  6  7  8  9 Right 10
pMakeMotifModelFromSSF:   8   Initial Left 10 Right  9
pMakeMotifModelFromSSF:   9   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 9
pUpdateModelWithSSF: IL_64048.1 allow insertions from initial node 8?
ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9920    0.0080    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_64048.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0564
   -6.0564

Timestamp 18-Jul-2025 22:48:30
pMakeSCFGModels: Making JAR3D model for motif group IL_64231.5, number 259 of 411
pMakeNodes starting loop:     a=4LFB|1|A|C|132 B=4LFB|1|A|G|230
  2 Basepair   132  230 CG cWW 
No need to probe because of interaction between a=4LFB|1|A|U|133 B=4LFB|1|A|U|229
  3 Basepair   133  229 UU cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|A|134 B=4LFB|1|A|A|228
    Insertion on left  4LFB|1|A|A|134
    Insertion on left  4LFB|1|A|C|135
    Insertion on right 4LFB|1|A|A|228
pMakeNodesProbeForInsertions:  a 4LFB|1|A|C|136 interacts with 4LFB|1|A|G|227
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|227 interacts with 4LFB|1|A|C|136
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|227 interacts with 4LFB|1|A|C|136
pMakeNodes probed for insert:  a=4LFB|1|A|C|136 B=4LFB|1|A|G|227
  4 Basepair   136  227 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|134
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|C|135
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|A|228
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C132 - G230 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UAC'
           RightLetter: 'AU'
               Comment: ' // Basepair U133 - U229 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|134'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|C|135'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|A|228'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C136 - G227 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_64231.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8220
   -8.5566
   -7.6403
   -7.6403
   -8.7301
   -7.0901
   -6.6789
  -10.4670
  -11.6222
   -9.5898
   -7.0901

Timestamp 18-Jul-2025 22:48:30
pMakeSCFGModels: Making JAR3D model for motif group IL_64403.1, number 260 of 411
pMakeNodes starting loop:     a=5U30|1|B|U|28 B=5U30|1|B|G|58
  2 Basepair    28   58 UG cWW 
pMakeNodes probe for inserts:  a=5U30|1|B|G|29 B=5U30|1|B|A|57
    Insertion on left  5U30|1|B|G|29
    Insertion on left  5U30|1|B|U|30
    Insertion on left  5U30|1|B|G|31
    Insertion on left  5U30|1|B|C|32
    Insertion on left  5U30|1|B|C|33
    Insertion on left  5U30|1|B|A|35
    Insertion on right 5U30|1|B|A|57
    Insertion on right 5U30|1|B|A|56
pMakeNodesProbeForInsertions:  a 5U30|1|B|G|37 interacts with 5U30|1|B|A|55
pMakeNodesProbeForInsertions:  B 5U30|1|B|A|55 interacts with 5U30|1|B|G|37
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5U30|1|B|A|55 interacts with 5U30|1|B|G|37
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5U30|1|B|G|37 B=5U30|1|B|A|55
  3 Basepair    37   55 GA cWW 
No need to probe because of interaction between a=5U30|1|B|G|38 B=5U30|1|B|C|54
  4 Basepair    38   54 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   5   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5U30|1|B|G|29
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5U30|1|B|U|30
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5U30|1|B|G|31
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5U30|1|B|C|32
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5U30|1|B|C|33
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5U30|1|B|A|34
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5U30|1|B|A|55
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5U30|1|B|C|54
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
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Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
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       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGUGCCA'
           RightLetter: 'AAG'
               Comment: ' // Basepair U28 - G58 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
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Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
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             Insertion: []
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        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5U30|1|B|G|29'
              NumLoops: []
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Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
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            RightIndex: 13
             Insertion: []
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
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                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
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Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
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        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: ''
               Comment: ' // Fixed node on left for 5U30|1|B|U|30'
              NumLoops: []
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                Delete: 1.0000e-03
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                     Z: []
           MiddleIndex: 10
                     P: []
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
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             LeftIndex: 4
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: ''
               Comment: ' // Fixed node on left for 5U30|1|B|G|31'
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                Delete: 1.0000e-03
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
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                     Z: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
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                    id: []
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        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
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                     P: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
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       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5U30|1|B|C|33'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
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                     Z: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
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             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5U30|1|B|A|34'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5U30|1|B|A|55'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
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                     Z: []
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                     P: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5U30|1|B|C|54'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
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                     Z: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G37 - A55 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                  rpar: [17×1 double]
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Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 21
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G38 - C54 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 23
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 13
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 13
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 13
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 13
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 13
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 13
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 13
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 13
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 13
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 13
pMakeMotifModelFromSSF:  16   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  17     Fixed Left  8 Right 12
pMakeMotifModelFromSSF:  18   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  19  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  20  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  21   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 21
pNextNodeJunction: Found a hairpin at node 21

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_64403.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.3733

Timestamp 18-Jul-2025 22:48:31
pMakeSCFGModels: Making JAR3D model for motif group IL_64842.1, number 261 of 411
pMakeNodes starting loop:     a=5ML7|1|B|C|2170 B=5ML7|1|B|G|2204
  2 Basepair  2170 2204 CG cWW 
pMakeNodes probe for inserts:  a=5ML7|1|B|A|2171 B=5ML7|1|B|A|2203
    Insertion on left  5ML7|1|B|A|2171
    Insertion on left  5ML7|1|B|C|2172
    Insertion on left  5ML7|1|B|U|2173
pMakeNodesProbeForInsertions:  a 5ML7|1|B|A|2174 interacts with 5ML7|1|B|A|2203
pMakeNodesProbeForInsertions:  B 5ML7|1|B|A|2203 interacts with 5ML7|1|B|A|2174
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5ML7|1|B|A|2203 interacts with 5ML7|1|B|A|2174
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5ML7|1|B|A|2174 B=5ML7|1|B|A|2203
pMakeNodes making a cluster near strand break a=5ML7|1|B|A|2174 B=5ML7|1|B|A|2203
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 6 and then 9 to 9
aa is 6 bb is 9
  3 Cluster   5ML7|1|B|A|2174:5ML7|1|B|C|2175 5ML7|1|B|A|2203:5ML7|1|B|A|2203
    LR Inter  5ML7|1|B|A|2174 5ML7|1|B|A|2203 tWH 
    LL Inter  5ML7|1|B|A|2174 5ML7|1|B|C|2175 cSH 
pMakeNodesCluster a=7 B=8 at the end
pMakeNodesCluster a=7 B=8 at the end
No need to probe because of interaction between a=5ML7|1|B|C|2177 B=5ML7|1|B|G|2202
  4 Basepair  2177 2202 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  5  6 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5ML7|1|B|A|2171
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5ML7|1|B|C|2172
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5ML7|1|B|U|2173
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CACU'
           RightLetter: 'G'
               Comment: ' // Basepair C2170 - G2204 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5ML7|1|B|A|2171'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2586

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5ML7|1|B|C|2172'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5ML7|1|B|U|2173'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 10
             LeftIndex: [5 6]
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AC'
           RightLetter: 'A'
               Comment: ' // Cluster node 5ML7|1|B|A|2174:5ML7|1|B|C|2175 and 5ML7|1|B|A|2203:5ML7|1|B|A|2203'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2586

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2177 - G2202 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   9   Cluster Left  5  6 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  12   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_64842.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4917

Timestamp 18-Jul-2025 22:48:31
pMakeSCFGModels: Making JAR3D model for motif group IL_64858.3, number 262 of 411
pMakeNodes starting loop:     a=8K85|1|B|A|40 B=8K85|1|A|U|14
  2 Basepair    40   14 AU cWW 
pMakeNodes probe for inserts:  a=8K85|1|B|G|41 B=8K85|1|A|G|13
    Insertion on right 8K85|1|A|G|13
pMakeNodesProbeForInsertions:  a 8K85|1|B|G|41 interacts with 8K85|1|A|G|8
pMakeNodesProbeForInsertions:  B 8K85|1|A|G|12 interacts with 8K85|1|B|G|46
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8K85|1|A|G|12 interacts with 8K85|1|A|G|8
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8K85|1|B|G|41 B=8K85|1|A|G|12
pMakeNodes making a cluster near strand break a=8K85|1|B|G|41 B=8K85|1|A|G|12
pMakeNodesCluster: amax is 12 bmin is 13, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 9 and then 16 to 20
aa is 9 bb is 16
  3 Cluster   8K85|1|B|G|41:8K85|1|B|G|50 8K85|1|A|G|7:8K85|1|A|G|12
    LR Inter  8K85|1|B|G|44 8K85|1|A|G|7 cWH 
    LR Inter  8K85|1|B|G|41 8K85|1|A|G|8 cWH 
    LR Inter  8K85|1|B|G|50 8K85|1|A|C|10 cWW 
    LR Inter  8K85|1|B|G|48 8K85|1|A|G|11 cHW 
    LR Inter  8K85|1|B|G|46 8K85|1|A|G|12 cHW 
    LL Inter  8K85|1|B|G|41 8K85|1|B|G|46 cHW 
    LL Inter  8K85|1|B|G|44 8K85|1|B|G|48 cHW 
    LL Inter  8K85|1|B|U|42 8K85|1|B|U|49 tSW 
    RR Inter  8K85|1|A|G|7 8K85|1|A|G|11 cWH 
    RR Inter  8K85|1|A|G|8 8K85|1|A|G|12 cWH 
    Left  strand conserved insertion 8K85|1|B|U|45 at position 4
pMakeNodesCluster a=10 B=15 at the end
pMakeNodesCluster a=10 B=15 at the end
No need to probe because of interaction between a=8K85|1|B|G|51 B=8K85|1|A|C|6
  4 Basepair    51    6 GC cWW 
No need to probe because of interaction between a=8K85|1|B|G|52 B=8K85|1|A|A|5
  5 Basepair    52    5 GA cWW 
No need to probe because of interaction between a=8K85|1|B|C|53 B=8K85|1|A|G|4
  6 Basepair    53    4 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 22
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 22
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8  9 Right 16 17 18 19 20
pMakeMotifModelFromSSF:   4  Basepair Left 10 Right 15
pMakeMotifModelFromSSF:   5  Basepair Left 11 Right 14
pMakeMotifModelFromSSF:   6  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:   7   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8K85|1|B|U|49
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 22
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [22×22 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 22
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'GU'
               Comment: ' // Basepair A40 - U14 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8K85|1|B|U|49'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×11 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: [1 2 3 4 5]
      InsertionComment: []
                IBases: [11×2 double]
    InteractionComment: {1×11 cell}
      JunctionDeletion: []
          InterIndices: [11×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 4
         RightNotInter: [1×0 double]
              NormCons: 0.0056

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [2 3 4 5 6 7 8 9]
            RightIndex: [16 17 18 19 20]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUGUGGUG'
           RightLetter: 'GGCGG'
               Comment: ' // Cluster node 8K85|1|B|G|41:8K85|1|B|G|50 and 8K85|1|A|G|7:8K85|1|A|G|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×11 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8]
                 Right: [1 2 3 4 5]
      InsertionComment: []
                IBases: [11×2 double]
    InteractionComment: {1×11 cell}
      JunctionDeletion: []
          InterIndices: [11×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 4
         RightNotInter: [1×0 double]
              NormCons: 0.0056

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 10
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 10
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G51 - C6 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G52 - A5 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 12
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C53 - G4 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 22
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 22
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 21
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 20
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6  7  8  9 Right 16 17 18 19 20
pMakeMotifModelFromSSF:   6   Initial Left 10 Right 15
pMakeMotifModelFromSSF:   7  Basepair Left 10 Right 15
pMakeMotifModelFromSSF:   8  Basepair Left 11 Right 14
pMakeMotifModelFromSSF:   9  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  10   Hairpin Left 13 Right 12
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_64858.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.7671
   -9.7671
   -9.1793
   -9.3055
  -10.7902
   -9.3055

Timestamp 18-Jul-2025 22:48:32
pMakeSCFGModels: Making JAR3D model for motif group IL_64900.1, number 263 of 411
pMakeNodes starting loop:     a=6HCT|1|E|C|2 B=6HCT|1|F|G|18
  2 Basepair     2   18 CG cWW 
No need to probe because of interaction between a=6HCT|1|E|C|3 B=6HCT|1|F|A|17
  3 Basepair     3   17 CA cWW 
No need to probe because of interaction between a=6HCT|1|E|G|4 B=6HCT|1|F|A|16
pMakeNodes making a cluster near strand break a=6HCT|1|E|G|4 B=6HCT|1|F|A|16
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 5 and then 12 to 12
aa is 5 bb is 12
  4 Cluster   6HCT|1|E|G|4:6HCT|1|E|G|7 6HCT|1|F|A|16:6HCT|1|F|A|16
    LR Inter  6HCT|1|E|G|4 6HCT|1|F|A|16 tSS 
    LR Inter  6HCT|1|E|G|7 6HCT|1|F|A|16 tSH 
    Left  strand conserved insertion 6HCT|1|E|A|5 at position 2
pMakeNodesCluster a=6 B=11 at the end
pMakeNodesCluster a=6 B=11 at the end
No need to probe because of interaction between a=6HCT|1|E|A|8 B=6HCT|1|F|G|15
  5 Basepair     8   15 AG tHS 
No need to probe because of interaction between a=6HCT|1|E|A|9 B=6HCT|1|F|U|14
  6 Basepair     9   14 AU tHS 
No need to probe because of interaction between a=6HCT|1|E|U|10 B=6HCT|1|F|A|13
  7 Basepair    10   13 UA cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   8   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2 - G18 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C3 - A17 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4 5]
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAG'
           RightLetter: 'A'
               Comment: ' // Cluster node 6HCT|1|E|G|4:6HCT|1|E|G|7 and 6HCT|1|F|A|16:6HCT|1|F|A|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.1817

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A8 - G15 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A9 - U14 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U10 - A13 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  6 Right 11
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   9   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_64900.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.4899
   -7.4899
   -7.4899

Timestamp 18-Jul-2025 22:48:32
pMakeSCFGModels: Making JAR3D model for motif group IL_65594.1, number 264 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|C|82 B=8P9A|1|AR|G|103
  2 Basepair    82  103 CG cWW 
No need to probe because of interaction between a=8P9A|1|AR|U|83 B=8P9A|1|AR|C|102
  3 Basepair    83  102 UC tSH 
No need to probe because of interaction between a=8P9A|1|AR|U|84 B=8P9A|1|AR|G|101
  4 Basepair    84  101 UG tSW 
No need to probe because of interaction between a=8P9A|1|AR|A|85 B=8P9A|1|AR|A|100
  5 Basepair    85  100 AA tHH 
pMakeNodes probe for inserts:  a=8P9A|1|AR|G|86 B=8P9A|1|AR|A|99
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|G|86 interacts with 8P9A|1|AR|U|87
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|A|99 interacts with 8P9A|1|AR|U|87
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|A|99 interacts with 8P9A|1|AR|U|87
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|AR|G|86 B=8P9A|1|AR|A|99
pMakeNodes making a cluster near strand break a=8P9A|1|AR|G|86 B=8P9A|1|AR|A|99
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 6 and then 11 to 11
aa is 6 bb is 11
  6 Cluster   8P9A|1|AR|G|86:8P9A|1|AR|U|87 8P9A|1|AR|A|99:8P9A|1|AR|A|99
    LR Inter  8P9A|1|AR|U|87 8P9A|1|AR|A|99 tWH 
    LL Inter  8P9A|1|AR|G|86 8P9A|1|AR|U|87 cSH 
pMakeNodesCluster a=7 B=10 at the end
pMakeNodesCluster a=7 B=10 at the end
No need to probe because of interaction between a=8P9A|1|AR|A|88 B=8P9A|1|AR|G|98
  7 Basepair    88   98 AG tHS 
No need to probe because of interaction between a=8P9A|1|AR|A|89 B=8P9A|1|AR|U|97
  8 Basepair    89   97 AU cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 12
pMakeMotifModelFromSSF:   6   Cluster Left  5  6 Right 11
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   9   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C82 - G103 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'C'
               Comment: ' // Basepair U83 - C102 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U84 - G101 tSW '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A85 - A100 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 7
             LeftIndex: [5 6]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 8P9A|1|AR|G|86:8P9A|1|AR|U|87 and 8P9A|1|AR|A|99:8P9A|1|AR|A|99'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A88 - G98 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A89 - U97 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 13
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 12
pMakeMotifModelFromSSF:   6   Cluster Left  5  6 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_65594.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.6488
   -8.2587

Timestamp 18-Jul-2025 22:48:32
pMakeSCFGModels: Making JAR3D model for motif group IL_65653.1, number 265 of 411
pMakeNodes starting loop:     a=8HZL|1|B|G|5 B=8HZL|1|B|C|80
pMakeNodes making a cluster near strand break a=8HZL|1|B|G|5 B=8HZL|1|B|C|80
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 7 and then 13 to 16
aa is 7 bb is 13
  2 Cluster   8HZL|1|B|G|5:8HZL|1|B|A|13 8HZL|1|B|A|77:8HZL|1|B|C|80
    LR Inter  8HZL|1|B|U|8 8HZL|1|B|A|77 tWH 
    LR Inter  8HZL|1|B|A|6 8HZL|1|B|A|79 tWW 
    LR Inter  8HZL|1|B|G|5 8HZL|1|B|C|80 cWW 
    LL Inter  8HZL|1|B|G|5 8HZL|1|B|A|12 tSW 
    LL Inter  8HZL|1|B|A|6 8HZL|1|B|A|13 tHW 
    RR Inter  8HZL|1|B|A|77 8HZL|1|B|C|78 cSH 
    Left  strand conserved insertion 8HZL|1|B|G|9 at position 4
    Left  strand conserved insertion 8HZL|1|B|A|11 at position 5
pMakeNodesCluster a=8 B=12 at the end
pMakeNodesCluster a=8 B=12 at the end
pMakeNodes probe for inserts:  a=8HZL|1|B|C|14 B=8HZL|1|B|G|76
    Insertion on left  8HZL|1|B|C|14
pMakeNodesProbeForInsertions:  a 8HZL|1|B|A|15 interacts with 8HZL|1|B|G|76
pMakeNodesProbeForInsertions:  B 8HZL|1|B|G|76 interacts with 8HZL|1|B|A|15
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8HZL|1|B|G|76 interacts with 8HZL|1|B|A|15
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  3 Initial     14 (1 insertion) and   76 (0 insertion)
pMakeNodes probed for insert:  a=8HZL|1|B|A|15 B=8HZL|1|B|G|76
  4 Basepair    15   76 AG tHS 
No need to probe because of interaction between a=8HZL|1|B|G|16 B=8HZL|1|B|C|75
  5 Basepair    16   75 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6  7 Right 13 14 15 16
pMakeMotifModelFromSSF:   3   Initial Left  8 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   6   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8HZL|1|B|A|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5 6 7]
            RightIndex: [13 14 15 16]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAUGAAA'
           RightLetter: 'ACAC'
               Comment: ' // Cluster node 8HZL|1|B|G|5:8HZL|1|B|A|13 and 8HZL|1|B|A|77:8HZL|1|B|C|80'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×8 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [8×2 double]
    InteractionComment: {1×8 cell}
      JunctionDeletion: []
          InterIndices: [8×2 double]
          LeftNotInter: [4 5]
         RightNotInter: [1×0 double]
              NormCons: 0.0242
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 8
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: []
               Comment: ' // Initial node 8HZL|1|B|C|14 - 8HZL|1|B|G|76 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 8
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8HZL|1|B|A|12'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 9
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A15 - G76 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G16 - C75 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6  7 Right 13 14 15 16
pMakeMotifModelFromSSF:   3   Initial Left  8 Right 12
pMakeMotifModelFromSSF:   4     Fixed Left  8 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  9 Right 12
pMakeMotifModelFromSSF:   6  Basepair Left  9 Right 12
pMakeMotifModelFromSSF:   7  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   8   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_65653.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.6613
   -7.6618
   -7.6618
   -7.6613

Timestamp 18-Jul-2025 22:48:33
pMakeSCFGModels: Making JAR3D model for motif group IL_65718.4, number 266 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|G|1760 B=8P9A|1|sR|C|1641
  2 Basepair  1760 1641 GC cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|U|1761 B=8P9A|1|sR|C|1640
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|U|1761 interacts with 8P9A|1|sR|A|1762
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|C|1640 interacts with 8P9A|1|sR|A|1762
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|C|1640 interacts with 8P9A|1|sR|A|1762
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|sR|U|1761 B=8P9A|1|sR|C|1640
pMakeNodes making a cluster near strand break a=8P9A|1|sR|U|1761 B=8P9A|1|sR|C|1640
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 3 and then 8 to 8
aa is 3 bb is 8
  3 Cluster   8P9A|1|sR|U|1761:8P9A|1|sR|A|1762 8P9A|1|sR|C|1640:8P9A|1|sR|C|1640
    LR Inter  8P9A|1|sR|A|1762 8P9A|1|sR|C|1640 cWS 
    LL Inter  8P9A|1|sR|U|1761 8P9A|1|sR|A|1762 cSH 
pMakeNodesCluster a=4 B=7 at the end
pMakeNodesCluster a=4 B=7 at the end
No need to probe because of interaction between a=8P9A|1|sR|A|1763 B=8P9A|1|sR|C|1639
  4 Basepair  1763 1639 AC cWW 
No need to probe because of interaction between a=8P9A|1|sR|C|1764 B=8P9A|1|sR|G|1638
  5 Basepair  1764 1638 CG cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1760 - C1641 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3]
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UA'
           RightLetter: 'C'
               Comment: ' // Cluster node 8P9A|1|sR|U|1761:8P9A|1|sR|A|1762 and 8P9A|1|sR|C|1640:8P9A|1|sR|C|1640'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.3277

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A1763 - C1639 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1764 - G1638 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  2  3 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_65718.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7065
   -5.7065
   -5.7065
   -5.7065

Timestamp 18-Jul-2025 22:48:33
pMakeSCFGModels: Making JAR3D model for motif group IL_65851.3, number 267 of 411
pMakeNodes starting loop:     a=3KTW|1|C|G|201 B=3KTW|1|C|C|222
  2 Basepair   201  222 GC cWW 
No need to probe because of interaction between a=3KTW|1|C|C|202 B=3KTW|1|C|A|221
  3 Basepair   202  221 CA cWW 
No need to probe because of interaction between a=3KTW|1|C|C|203 B=3KTW|1|C|A|220
pMakeNodes making a cluster near strand break a=3KTW|1|C|C|203 B=3KTW|1|C|A|220
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 4 and then 11 to 12
aa is 4 bb is 11
  4 Cluster   3KTW|1|C|C|203:3KTW|1|C|A|204 3KTW|1|C|C|219:3KTW|1|C|A|220
    LR Inter  3KTW|1|C|C|203 3KTW|1|C|C|219 tWH 
    LR Inter  3KTW|1|C|A|204 3KTW|1|C|C|219 tHW 
    LR Inter  3KTW|1|C|C|203 3KTW|1|C|A|220 tSH 
pMakeNodesCluster a=5 B=10 at the end
pMakeNodesCluster a=5 B=10 at the end
No need to probe because of interaction between a=3KTW|1|C|G|205 B=3KTW|1|C|G|218
  5 Basepair   205  218 GG tHS 
No need to probe because of interaction between a=3KTW|1|C|G|206 B=3KTW|1|C|A|217
  6 Basepair   206  217 GA cWW 
No need to probe because of interaction between a=3KTW|1|C|C|207 B=3KTW|1|C|G|216
  7 Basepair   207  216 CG cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  3  4 Right 11 12
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G201 - C222 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C202 - A221 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4]
            RightIndex: [11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CA'
           RightLetter: 'CA'
               Comment: ' // Cluster node 3KTW|1|C|C|203:3KTW|1|C|A|204 and 3KTW|1|C|C|219:3KTW|1|C|A|220'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0806

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G205 - G218 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G206 - A217 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C207 - G216 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  3  4 Right 11 12
pMakeMotifModelFromSSF:   5   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_65851.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7492
   -5.7492

Timestamp 18-Jul-2025 22:48:33
pMakeSCFGModels: Making JAR3D model for motif group IL_66635.5, number 268 of 411
pMakeNodes starting loop:     a=6XH2|1|D|A|22 B=6XH2|1|D|U|40
  2 Basepair    22   40 AU cWW 
pMakeNodes probe for inserts:  a=6XH2|1|D|U|23 B=6XH2|1|D|C|39
    Insertion on left  6XH2|1|D|U|23
pMakeNodesProbeForInsertions:  a 6XH2|1|D|G|26 interacts with 6XH2|1|D|C|39
pMakeNodesProbeForInsertions:  B 6XH2|1|D|C|39 interacts with 6XH2|1|D|G|26
pMakeNodesProbeForInsertions:  B 6XH2|1|D|C|39 interacts with 6XH2|1|D|G|26
pMakeNodes probed for insert:  a=6XH2|1|D|G|26 B=6XH2|1|D|C|39
  3 Basepair    26   39 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6XH2|1|D|U|23
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AU'
           RightLetter: 'U'
               Comment: ' // Basepair A22 - U40 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6XH2|1|D|U|23'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G26 - C39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_66635.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.4799
   -5.8546
   -6.0389
   -5.5966
   -7.7037
   -5.7706
   -6.5108
   -6.7635
   -5.0073
   -7.0630
   -5.1066
   -6.1276
   -5.3284
   -5.0422
   -5.3284
   -5.1066
   -5.3284
   -5.7605
   -4.7234
   -5.3284
   -5.7605
   -5.1527
   -6.5108
   -5.0420
   -5.1527
   -6.5567
   -6.2403

Timestamp 18-Jul-2025 22:48:33
pMakeSCFGModels: Making JAR3D model for motif group IL_66663.1, number 269 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|G|1415 B=8CRE|1|CM|C|1264
  2 Basepair  1415 1264 GC cWW 
pMakeNodes probe for inserts:  a=8CRE|1|CM|U|1416 B=8CRE|1|CM|G|1263
    Insertion on left  8CRE|1|CM|U|1416
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|C|1417 interacts with 8CRE|1|CM|A|1260
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|1263 interacts with 8CRE|1|CM|G|1419
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|1263 interacts with 8CRE|1|CM|G|1419
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8CRE|1|CM|C|1417 B=8CRE|1|CM|G|1263
pMakeNodes making a cluster near strand break a=8CRE|1|CM|C|1417 B=8CRE|1|CM|G|1263
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 7 and then 11 to 14
aa is 7 bb is 11
  3 Cluster   8CRE|1|CM|C|1417:8CRE|1|CM|U|1423 8CRE|1|CM|A|1260:8CRE|1|CM|G|1263
    LR Inter  8CRE|1|CM|C|1417 8CRE|1|CM|A|1260 tWH 
    LR Inter  8CRE|1|CM|U|1423 8CRE|1|CM|A|1260 cSW 
    LR Inter  8CRE|1|CM|A|1422 8CRE|1|CM|U|1261 cWW 
    LR Inter  8CRE|1|CM|G|1419 8CRE|1|CM|G|1263 tHS 
    LL Inter  8CRE|1|CM|C|1417 8CRE|1|CM|U|1423 tSW 
    Left  strand conserved insertion 8CRE|1|CM|U|1420 at position 3
    Right strand conserved insertion 8CRE|1|CM|G|1262 at position 3
pMakeNodesCluster a=8 B=10 at the end
pMakeNodesCluster a=8 B=10 at the end
pMakeNodes probe for inserts:  a=8CRE|1|CM|G|1424 B=8CRE|1|CM|G|1258
    Insertion on right 8CRE|1|CM|G|1258
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|G|1424 interacts with 8CRE|1|CM|U|1257
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|U|1257 interacts with 8CRE|1|CM|G|1424
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|U|1257 interacts with 8CRE|1|CM|G|1424
  4 Initial   1424 (0 insertion) and 1258 (1 insertion)
pMakeNodes probed for insert:  a=8CRE|1|CM|G|1424 B=8CRE|1|CM|U|1257
  5 Basepair  1424 1257 GU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3   Cluster Left  3  4  5  6  7 Right 11 12 13 14
pMakeMotifModelFromSSF:   4   Initial Left  8 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   6   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|G|1258
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|CM|U|1416
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GU'
           RightLetter: 'C'
               Comment: ' // Basepair G1415 - C1264 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|G|1258'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 3
         RightNotInter: 3
              NormCons: 0.0328

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [3 4 5 6 7]
            RightIndex: [11 12 13 14]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CGUAU'
           RightLetter: 'AUGG'
               Comment: ' // Cluster node 8CRE|1|CM|C|1417:8CRE|1|CM|U|1423 and 8CRE|1|CM|A|1260:8CRE|1|CM|G|1263'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 3
         RightNotInter: 3
              NormCons: 0.0328

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: 'G'
               Comment: ' // Initial node 8CRE|1|CM|G|1424 - 8CRE|1|CM|G|1258 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|CM|U|1416'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1424 - U1257 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 14
pMakeMotifModelFromSSF:   5   Cluster Left  3  4  5  6  7 Right 11 12 13 14
pMakeMotifModelFromSSF:   6   Initial Left  8 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  8 Right  9
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pConservedInteractionList: did not find a substitution probability matrix for cWH  between 10 and 13
pConservedInteractionList: did not find a substitution probability matrix for cWH  between 10 and 13
pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_66663.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.0172

Timestamp 18-Jul-2025 22:48:34
pMakeSCFGModels: Making JAR3D model for motif group IL_66798.2, number 270 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|U|606 B=9DFE|1|1A|G|622
  2 Basepair   606  622 UG cWW 
pMakeNodes probe for inserts:  a=9DFE|1|1A|U|607 B=9DFE|1|1A|A|621
    Insertion on left  9DFE|1|1A|U|607
    Insertion on left  9DFE|1|1A|A|608
    Insertion on right 9DFE|1|1A|A|621
    Insertion on right 9DFE|1|1A|G|620
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|A|609 interacts with 9DFE|1|1A|G|619
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|G|619 interacts with 9DFE|1|1A|A|609
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|G|619 interacts with 9DFE|1|1A|A|609
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=9DFE|1|1A|A|609 B=9DFE|1|1A|G|619
  3 Basepair   609  619 AG tHS 
No need to probe because of interaction between a=9DFE|1|1A|G|610 B=9DFE|1|1A|C|618
  4 Basepair   610  618 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|U|607
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|A|608
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 9DFE|1|1A|A|621
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 9DFE|1|1A|G|620
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UUA'
           RightLetter: 'GAG'
               Comment: ' // Basepair U606 - G622 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|U|607'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|A|608'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 9DFE|1|1A|A|621'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 9DFE|1|1A|G|620'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A609 - G619 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G610 - C618 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  4 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_66798.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.8384
   -4.8406
   -4.8384
   -5.6672
   -5.6816
   -7.0324

Timestamp 18-Jul-2025 22:48:34
pMakeSCFGModels: Making JAR3D model for motif group IL_66997.2, number 271 of 411
pMakeNodes starting loop:     a=4YAZ|1|R|G|77 B=4YAZ|1|R|C|7
pMakeNodes making a cluster near strand break a=4YAZ|1|R|G|77 B=4YAZ|1|R|C|7
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 3 and then 8 to 8
aa is 3 bb is 8
  2 Cluster   4YAZ|1|R|G|77:4YAZ|1|R|A|79 4YAZ|1|R|C|7:4YAZ|1|R|C|7
    LR Inter  4YAZ|1|R|G|77 4YAZ|1|R|C|7 cWW 
    LR Inter  4YAZ|1|R|A|79 4YAZ|1|R|C|7 cWS 
    LL Inter  4YAZ|1|R|G|77 4YAZ|1|R|A|78 cSH 
pMakeNodesCluster a=4 B=7 at the end
pMakeNodesCluster a=4 B=7 at the end
pMakeNodes probe for inserts:  a=4YAZ|1|R|A|80 B=4YAZ|1|R|A|6
    Insertion on left  4YAZ|1|R|A|80
    Insertion on right 4YAZ|1|R|A|6
pMakeNodesProbeForInsertions:  a 4YAZ|1|R|U|81 interacts with 4YAZ|1|R|A|4
pMakeNodesProbeForInsertions:  B 4YAZ|1|R|A|4 interacts with 4YAZ|1|R|U|81
pMakeNodesProbeForInsertions:  B 4YAZ|1|R|A|4 interacts with 4YAZ|1|R|U|81
  3 Initial     80 (1 insertion) and    6 (1 insertion)
pMakeNodes probed for insert:  a=4YAZ|1|R|U|81 B=4YAZ|1|R|A|4
  4 Basepair    81    4 UA cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  8
pMakeMotifModelFromSSF:   3   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4YAZ|1|R|C|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4YAZ|1|R|A|79
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 0 0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3]
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAA'
           RightLetter: 'C'
               Comment: ' // Cluster node 4YAZ|1|R|G|77:4YAZ|1|R|A|79 and 4YAZ|1|R|C|7:4YAZ|1|R|C|7'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0628
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Initial node 4YAZ|1|R|A|80 - 4YAZ|1|R|A|6 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4YAZ|1|R|C|7'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4YAZ|1|R|A|79'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U81 - A4 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  8
pMakeMotifModelFromSSF:   3   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   4     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   5   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   6     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_66997.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.2688
   -5.8873

Timestamp 18-Jul-2025 22:48:34
pMakeSCFGModels: Making JAR3D model for motif group IL_67095.2, number 272 of 411
pMakeNodes starting loop:     a=4WF9|1|X|U|1707 B=4WF9|1|X|A|2024
  2 Basepair  1707 2024 UA cWW 
No need to probe because of interaction between a=4WF9|1|X|A|1708 B=4WF9|1|X|C|2023
  3 Basepair  1708 2023 AC tWW 
No need to probe because of interaction between a=4WF9|1|X|A|1709 B=4WF9|1|X|U|2022
  4 Basepair  1709 2022 AU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1707 - A2024 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A1708 - C2023 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A1709 - U2022 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_67095.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.1758
   -4.2571
   -4.1758
   -4.3138
   -4.2571
   -4.3086
   -4.1754
   -9.2974

Timestamp 18-Jul-2025 22:48:34
pMakeSCFGModels: Making JAR3D model for motif group IL_67623.1, number 273 of 411
pMakeNodes starting loop:     a=4V9F|1|9|G|21 B=4V9F|1|9|C|59
  2 Basepair    21   59 GC cWW 
No need to probe because of interaction between a=4V9F|1|9|G|22 B=4V9F|1|9|G|58
pMakeNodes making a cluster near strand break a=4V9F|1|9|G|22 B=4V9F|1|9|G|58
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 6 and then 13 to 13
aa is 6 bb is 13
  3 Cluster   4V9F|1|9|G|22:4V9F|1|9|C|26 4V9F|1|9|G|58:4V9F|1|9|G|58
    LR Inter  4V9F|1|9|G|22 4V9F|1|9|G|58 bif 
    LL Inter  4V9F|1|9|G|22 4V9F|1|9|C|26 tSW 
    Left  strand conserved insertion 4V9F|1|9|U|23 at position 2
    Left  strand conserved insertion 4V9F|1|9|U|24 at position 3
    Left  strand conserved insertion 4V9F|1|9|G|25 at position 4
pMakeNodesCluster a=7 B=12 at the end
pMakeNodesCluster a=7 B=12 at the end
pMakeNodes probe for inserts:  a=4V9F|1|9|C|27 B=4V9F|1|9|A|57
pMakeNodesProbeForInsertions:  a 4V9F|1|9|C|27 interacts with 4V9F|1|9|U|55
pMakeNodesProbeForInsertions:  B 4V9F|1|9|A|57 interacts with 4V9F|1|9|U|28
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4V9F|1|9|A|57 interacts with 4V9F|1|9|U|55
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  4 Initial     27 (0 insertion) and   57 (0 insertion)
pMakeNodes probed for insert:  a=4V9F|1|9|C|27 B=4V9F|1|9|A|57
pMakeNodes making a cluster near strand break a=4V9F|1|9|C|27 B=4V9F|1|9|A|57
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 7 to 8 and then 9 to 12
aa is 8 bb is 9
  5 Cluster   4V9F|1|9|C|27:4V9F|1|9|U|28 4V9F|1|9|A|54:4V9F|1|9|A|57
    LR Inter  4V9F|1|9|U|28 4V9F|1|9|A|54 cWW 
    LR Inter  4V9F|1|9|C|27 4V9F|1|9|U|55 cWW 
    LR Inter  4V9F|1|9|U|28 4V9F|1|9|A|57 cSW 
    RR Inter  4V9F|1|9|U|55 4V9F|1|9|A|57 cSH 
    Right strand conserved insertion 4V9F|1|9|A|56 at position 3
pMakeNodesCluster a=9 B=8 at the end
pMakeNodesCluster a=9 B=8 at the end
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  7 Right 12
pMakeMotifModelFromSSF:   5   Cluster Left  7  8 Right  9 10 11 12
pMakeMotifModelFromSSF:   6   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G21 - C59 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5 6]
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUUGC'
           RightLetter: 'G'
               Comment: ' // Cluster node 4V9F|1|9|G|22:4V9F|1|9|C|26 and 4V9F|1|9|G|58:4V9F|1|9|G|58'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 0.3741

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 4V9F|1|9|C|27 - 4V9F|1|9|A|57 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [7 8]
            RightIndex: [9 10 11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CU'
           RightLetter: 'AUAA'
               Comment: ' // Cluster node 4V9F|1|9|C|27:4V9F|1|9|U|28 and 4V9F|1|9|A|54:4V9F|1|9|A|57'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: [1 2 3 4]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: 3
              NormCons: 0.0214

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  7 Right 12
pMakeMotifModelFromSSF:   5   Cluster Left  7  8 Right  9 10 11 12
pMakeMotifModelFromSSF:   6   Initial Left  9 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 7
pUpdateModelWithSSF: IL_67623.1 allow insertions from initial node 6?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_67623.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1591

Timestamp 18-Jul-2025 22:48:34
pMakeSCFGModels: Making JAR3D model for motif group IL_67767.4, number 274 of 411
pMakeNodes starting loop:     a=5VCI|1|A|C|8 B=5VCI|1|B|G|5
  2 Basepair     8    5 CG cWW 
pMakeNodes probe for inserts:  a=5VCI|1|A|U|9 B=5VCI|1|B|U|4
pMakeNodesProbeForInsertions:  a 5VCI|1|A|U|9 interacts with 5VCI|1|B|A|3
pMakeNodesProbeForInsertions:  B 5VCI|1|B|U|4 interacts with 5VCI|1|A|A|11
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5VCI|1|B|U|4 interacts with 5VCI|1|A|A|11
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5VCI|1|A|U|9 B=5VCI|1|B|U|4
pMakeNodes making a cluster near strand break a=5VCI|1|A|U|9 B=5VCI|1|B|U|4
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 7 to 8
aa is 4 bb is 7
  3 Cluster   5VCI|1|A|U|9:5VCI|1|A|A|11 5VCI|1|B|A|3:5VCI|1|B|U|4
    LR Inter  5VCI|1|A|U|9 5VCI|1|B|A|3 tWH 
    LR Inter  5VCI|1|A|A|11 5VCI|1|B|U|4 cWW 
    LL Inter  5VCI|1|A|A|10 5VCI|1|A|A|11 cSH 
pMakeNodesCluster a=5 B=6 at the end
pMakeNodesCluster a=5 B=6 at the end
No need to probe because of interaction between a=5VCI|1|A|G|12 B=5VCI|1|B|U|2
  4 Basepair    12    2 GU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  7  8
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C8 - G5 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4]
            RightIndex: [7 8]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAA'
           RightLetter: 'AU'
               Comment: ' // Cluster node 5VCI|1|A|U|9:5VCI|1|A|A|11 and 5VCI|1|B|A|3:5VCI|1|B|U|4'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2468

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G12 - U2 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  7  8
pMakeMotifModelFromSSF:   4   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_67767.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.1338
   -4.1338
   -4.1338
   -4.1338
   -4.1338
   -4.1338
   -4.1338

Timestamp 18-Jul-2025 22:48:35
pMakeSCFGModels: Making JAR3D model for motif group IL_67780.1, number 275 of 411
pMakeNodes starting loop:     a=4WF9|1|X|G|1476 B=4WF9|1|X|C|1608
pMakeNodes making a cluster near strand break a=4WF9|1|X|G|1476 B=4WF9|1|X|C|1608
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 1 and then 8 to 10
aa is 1 bb is 8
  2 Cluster   4WF9|1|X|G|1476:4WF9|1|X|G|1476 4WF9|1|X|C|1606:4WF9|1|X|C|1608
    LR Inter  4WF9|1|X|G|1476 4WF9|1|X|C|1608 cWW 
    RR Inter  4WF9|1|X|C|1606 4WF9|1|X|C|1608 cSH 
    Right strand conserved insertion 4WF9|1|X|A|1607 at position 2
pMakeNodesCluster a=2 B=7 at the end
pMakeNodesCluster a=2 B=7 at the end
pMakeNodes probe for inserts:  a=4WF9|1|X|U|1477 B=4WF9|1|X|A|1605
    Insertion on left  4WF9|1|X|U|1477
    Insertion on left  4WF9|1|X|A|1478
    Insertion on right 4WF9|1|X|A|1605
pMakeNodesProbeForInsertions:  a 4WF9|1|X|G|1479 interacts with 4WF9|1|X|C|1604
pMakeNodesProbeForInsertions:  B 4WF9|1|X|C|1604 interacts with 4WF9|1|X|G|1479
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4WF9|1|X|C|1604 interacts with 4WF9|1|X|G|1480
  3 Initial   1477 (2 insertion) and 1605 (1 insertion)
pMakeNodes probed for insert:  a=4WF9|1|X|G|1479 B=4WF9|1|X|C|1604
pMakeNodes making a cluster near strand break a=4WF9|1|X|G|1479 B=4WF9|1|X|C|1604
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 6 to 6
aa is 5 bb is 6
  4 Cluster   4WF9|1|X|G|1479:4WF9|1|X|G|1480 4WF9|1|X|C|1604:4WF9|1|X|C|1604
    LR Inter  4WF9|1|X|G|1479 4WF9|1|X|C|1604 cWW 
    LR Inter  4WF9|1|X|G|1480 4WF9|1|X|C|1604 cWW 
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right  8  9 10
pMakeMotifModelFromSSF:   3   Initial Left  2 Right  7
pMakeMotifModelFromSSF:   4   Cluster Left  4  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|U|1477
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|A|1478
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4WF9|1|X|A|1605
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: 1
            RightIndex: [8 9 10]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'G'
           RightLetter: 'CAC'
               Comment: ' // Cluster node 4WF9|1|X|G|1476:4WF9|1|X|G|1476 and 4WF9|1|X|C|1606:4WF9|1|X|C|1608'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: 2
              NormCons: 0.2509

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: 'A'
               Comment: ' // Initial node 4WF9|1|X|U|1477 - 4WF9|1|X|A|1605 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|U|1477'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2502

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|A|1478'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4WF9|1|X|A|1605'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 11
             LeftIndex: [4 5]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GG'
           RightLetter: 'C'
               Comment: ' // Cluster node 4WF9|1|X|G|1479:4WF9|1|X|G|1480 and 4WF9|1|X|C|1604:4WF9|1|X|C|1604'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2502

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2   Cluster Left  1 Right  8  9 10
pMakeMotifModelFromSSF:   3   Initial Left  2 Right  7
pMakeMotifModelFromSSF:   4     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   5   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   6     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   8     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  4 Right  6
pMakeMotifModelFromSSF:  10   Cluster Left  4  5 Right  6
pMakeMotifModelFromSSF:  11   Initial Left  6 Right  5
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 12
pUpdateModelWithSSF: IL_67780.1 allow insertions from initial node 11?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_67780.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8769

Timestamp 18-Jul-2025 22:48:35
pMakeSCFGModels: Making JAR3D model for motif group IL_68140.4, number 276 of 411
pMakeNodes starting loop:     a=1S03|1|A|A|12 B=1S03|1|A|U|38
pMakeNodes making a cluster near strand break a=1S03|1|A|A|12 B=1S03|1|A|U|38
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 3 and then 6 to 6
aa is 3 bb is 6
  2 Cluster   1S03|1|A|A|12:1S03|1|A|A|14 1S03|1|A|U|38:1S03|1|A|U|38
    LR Inter  1S03|1|A|A|12 1S03|1|A|U|38 cWW 
    LR Inter  1S03|1|A|A|14 1S03|1|A|U|38 cWS 
    LL Inter  1S03|1|A|A|13 1S03|1|A|A|14 cSH 
pMakeNodesCluster a=4 B=5 at the end
pMakeNodesCluster a=4 B=5 at the end
No need to probe because of interaction between a=1S03|1|A|C|15 B=1S03|1|A|G|37
  3 Basepair    15   37 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 0 0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAA'
           RightLetter: 'U'
               Comment: ' // Cluster node 1S03|1|A|A|12:1S03|1|A|A|14 and 1S03|1|A|U|38:1S03|1|A|U|38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0758
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C15 - G37 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  6
pMakeMotifModelFromSSF:   3   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_68140.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.8507
   -3.8507
   -4.3272
   -4.3776
   -4.3272
   -4.3272
   -3.4603
   -3.4603
   -3.2629
   -3.2629
   -3.2629
   -3.2629
   -3.2629
   -3.2629
   -3.2629
   -3.9368
   -4.1258
   -6.7433

Timestamp 18-Jul-2025 22:48:35
pMakeSCFGModels: Making JAR3D model for motif group IL_68243.1, number 277 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|C|844 B=9DFE|1|1A|G|934
  2 Basepair   844  934 CG cWW 
No need to probe because of interaction between a=9DFE|1|1A|G|845 B=9DFE|1|1A|A|933
pMakeNodes making a cluster near strand break a=9DFE|1|1A|G|845 B=9DFE|1|1A|A|933
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 11 to 12
aa is 4 bb is 11
  3 Cluster   9DFE|1|1A|G|845:9DFE|1|1A|U|847 9DFE|1|1A|G|931:9DFE|1|1A|A|933
    LR Inter  9DFE|1|1A|C|846 9DFE|1|1A|G|931 cWW 
    LR Inter  9DFE|1|1A|G|845 9DFE|1|1A|A|933 cHW 
    LR Inter  9DFE|1|1A|U|847 9DFE|1|1A|A|933 cWW 
pMakeNodesCluster a=5 B=10 at the end
pMakeNodesCluster a=5 B=10 at the end
pMakeNodes probe for inserts:  a=9DFE|1|1A|G|848 B=9DFE|1|1A|U|930
    Insertion on left  9DFE|1|1A|G|848
    Insertion on right 9DFE|1|1A|U|930
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|A|849 interacts with 9DFE|1|1A|G|928
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|G|928 interacts with 9DFE|1|1A|A|849
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|G|928 interacts with 9DFE|1|1A|A|849
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  4 Initial    848 (1 insertion) and  930 (1 insertion)
pMakeNodes probed for insert:  a=9DFE|1|1A|A|849 B=9DFE|1|1A|G|928
  5 Basepair   849  928 AG tHS 
No need to probe because of interaction between a=9DFE|1|1A|C|850 B=9DFE|1|1A|G|927
  6 Basepair   850  927 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 11 12
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|G|848
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 9DFE|1|1A|U|930
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C844 - G934 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4]
            RightIndex: [11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GCU'
           RightLetter: 'GA'
               Comment: ' // Cluster node 9DFE|1|1A|G|845:9DFE|1|1A|U|847 and 9DFE|1|1A|G|931:9DFE|1|1A|A|933'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2538

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Initial node 9DFE|1|1A|G|848 - 9DFE|1|1A|U|930 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|G|848'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 9DFE|1|1A|U|930'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A849 - G928 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C850 - G927 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 11 12
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  10  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  11   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 11
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 1 of 1, pair 2,12 for nucleotide 2 (G) making self BPh with edge 1
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_68243.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.1763

Timestamp 18-Jul-2025 22:48:35
pMakeSCFGModels: Making JAR3D model for motif group IL_68405.1, number 278 of 411
pMakeNodes starting loop:     a=2R8S|1|R|C|121 B=2R8S|1|R|G|200
  2 Basepair   121  200 CG cWW 
pMakeNodes probe for inserts:  a=2R8S|1|R|A|122 B=2R8S|1|R|A|198
    Insertion on left  2R8S|1|R|A|122
pMakeNodesProbeForInsertions:  a 2R8S|1|R|A|123 interacts with 2R8S|1|R|A|198
pMakeNodesProbeForInsertions:  B 2R8S|1|R|A|198 interacts with 2R8S|1|R|A|123
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 2R8S|1|R|A|198 interacts with 2R8S|1|R|A|123
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=2R8S|1|R|A|123 B=2R8S|1|R|A|198
  3 Basepair   123  198 AA tWH 
No need to probe because of interaction between a=2R8S|1|R|C|124 B=2R8S|1|R|C|197
  4 Basepair   124  197 CC tHW 
No need to probe because of interaction between a=2R8S|1|R|G|126 B=2R8S|1|R|A|196
  5 Basepair   126  196 GA cWW 
No need to probe because of interaction between a=2R8S|1|R|C|127 B=2R8S|1|R|G|195
  6 Basepair   127  195 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2R8S|1|R|A|122
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: 'G'
               Comment: ' // Basepair C121 - G200 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2R8S|1|R|A|122'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A123 - A198 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C124 - C197 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G126 - A196 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C127 - G195 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_68405.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.7027

Timestamp 18-Jul-2025 22:48:36
pMakeSCFGModels: Making JAR3D model for motif group IL_68574.4, number 279 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|U|1468 B=5J7L|1|DA|G|1524
  2 Basepair  1468 1524 UG cWW 
No need to probe because of interaction between a=5J7L|1|DA|A|1469 B=5J7L|1|DA|A|1522
  3 Basepair  1469 1522 AA tHH 
No need to probe because of interaction between a=5J7L|1|DA|A|1470 B=5J7L|1|DA|G|1521
  4 Basepair  1470 1521 AG tHS 
No need to probe because of interaction between a=5J7L|1|DA|G|1471 B=5J7L|1|DA|U|1520
  5 Basepair  1471 1520 GU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U1468 - G1524 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A1469 - A1522 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1470 - G1521 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1471 - U1520 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_68574.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.9744
   -5.7960
   -8.4575

Timestamp 18-Jul-2025 22:48:36
pMakeSCFGModels: Making JAR3D model for motif group IL_68909.1, number 280 of 411
pMakeNodes starting loop:     a=1J2B|1|C|G|943 B=1J2B|1|C|C|929
  2 Basepair   943  929 GC cWW 
No need to probe because of interaction between a=1J2B|1|C|G|944 B=1J2B|1|C|C|928
  3 Basepair   944  928 GC cWW 
No need to probe because of interaction between a=1J2B|1|C|A|945 B=1J2B|1|C|G|927
  4 Basepair   945  927 AG cWW 
pMakeNodes probe for inserts:  a=1J2B|1|C|G|946 B=1J2B|1|C|C|926
    Insertion on left  1J2B|1|C|G|946
pMakeNodesProbeForInsertions:  a 1J2B|1|C|G|947 interacts with 1J2B|1|C|C|926
pMakeNodesProbeForInsertions:  B 1J2B|1|C|C|926 interacts with 1J2B|1|C|G|947
pMakeNodesProbeForInsertions:  B 1J2B|1|C|C|926 interacts with 1J2B|1|C|G|947
pMakeNodes probed for insert:  a=1J2B|1|C|G|947 B=1J2B|1|C|C|926
  5 Basepair   947  926 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1J2B|1|C|C|929
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G943 - C929 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G944 - C928 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: 'G'
               Comment: ' // Basepair A945 - G927 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1J2B|1|C|C|929'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G947 - C926 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_68909.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.9132
   -9.6530
   -8.7029
  -10.3558
  -12.6506
  -13.2302

Timestamp 18-Jul-2025 22:48:36
pMakeSCFGModels: Making JAR3D model for motif group IL_69000.1, number 281 of 411
pMakeNodes starting loop:     a=9C2K|1|R|G|9 B=9C2K|1|R|C|32
  2 Basepair     9   32 GC cWW 
pMakeNodes probe for inserts:  a=9C2K|1|R|G|10 B=9C2K|1|R|A|31
    Insertion on left  9C2K|1|R|G|10
    Insertion on left  9C2K|1|R|G|11
    Insertion on left  9C2K|1|R|C|12
pMakeNodesProbeForInsertions:  a 9C2K|1|R|G|13 interacts with 9C2K|1|R|A|31
pMakeNodesProbeForInsertions:  B 9C2K|1|R|A|31 interacts with 9C2K|1|R|G|13
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 9C2K|1|R|A|31 interacts with 9C2K|1|R|G|13
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=9C2K|1|R|G|13 B=9C2K|1|R|A|31
  3 Basepair    13   31 GA cWW 
No need to probe because of interaction between a=9C2K|1|R|C|14 B=9C2K|1|R|G|30
  4 Basepair    14   30 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9C2K|1|R|G|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9C2K|1|R|G|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9C2K|1|R|C|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGGC'
           RightLetter: 'C'
               Comment: ' // Basepair G9 - C32 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9C2K|1|R|G|10'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9C2K|1|R|G|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9C2K|1|R|C|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G13 - A31 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C14 - G30 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_69000.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.3967
   -5.3967

Timestamp 18-Jul-2025 22:48:36
pMakeSCFGModels: Making JAR3D model for motif group IL_69145.3, number 282 of 411
pMakeNodes starting loop:     a=5FJC|1|A|U|64 B=5FJC|1|A|A|85
  2 Basepair    64   85 UA cWW 
pMakeNodes probe for inserts:  a=5FJC|1|A|C|65 B=5FJC|1|A|A|84
    Insertion on left  5FJC|1|A|C|65
    Insertion on left  5FJC|1|A|C|66
    Insertion on left  5FJC|1|A|U|67
    Insertion on left  5FJC|1|A|G|68
    Insertion on right 5FJC|1|A|A|84
    Insertion on right 5FJC|1|A|A|83
pMakeNodesProbeForInsertions:  a 5FJC|1|A|C|69 interacts with 5FJC|1|A|G|82
pMakeNodesProbeForInsertions:  B 5FJC|1|A|G|82 interacts with 5FJC|1|A|C|69
pMakeNodesProbeForInsertions:  B 5FJC|1|A|G|82 interacts with 5FJC|1|A|C|69
pMakeNodes probed for insert:  a=5FJC|1|A|C|69 B=5FJC|1|A|G|82
  3 Basepair    69   82 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5FJC|1|A|C|65
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5FJC|1|A|C|66
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5FJC|1|A|U|67
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5FJC|1|A|G|68
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5FJC|1|A|A|84
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5FJC|1|A|A|83
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UCCUG'
           RightLetter: 'AAA'
               Comment: ' // Basepair U64 - A85 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5FJC|1|A|C|65'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5FJC|1|A|C|66'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5FJC|1|A|U|67'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5FJC|1|A|G|68'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5FJC|1|A|A|84'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5FJC|1|A|A|83'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C69 - G82 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 18
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  9
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  13     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  14   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  15  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  16   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a hairpin at node 16

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_69145.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.2307
   -4.2307
   -5.9253
   -4.2307

Timestamp 18-Jul-2025 22:48:36
pMakeSCFGModels: Making JAR3D model for motif group IL_69229.3, number 283 of 411
pMakeNodes starting loop:     a=3NVI|1|F|G|15 B=3NVI|1|F|C|8
  2 Basepair    15    8 GC cWW 
No need to probe because of interaction between a=3NVI|1|F|C|16 B=3NVI|1|F|A|7
pMakeNodes making a cluster near strand break a=3NVI|1|F|C|16 B=3NVI|1|F|A|7
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 11 to 11
aa is 4 bb is 11
  3 Cluster   3NVI|1|F|C|16:3NVI|1|F|G|19 3NVI|1|F|A|7:3NVI|1|F|A|7
    LR Inter  3NVI|1|F|C|16 3NVI|1|F|A|7 tSS 
    LR Inter  3NVI|1|F|G|19 3NVI|1|F|A|7 tSH 
    Left  strand conserved insertion 3NVI|1|F|G|17 at position 2
pMakeNodesCluster a=5 B=10 at the end
pMakeNodesCluster a=5 B=10 at the end
No need to probe because of interaction between a=3NVI|1|F|A|20 B=3NVI|1|F|G|6
  4 Basepair    20    6 AG tHS 
No need to probe because of interaction between a=3NVI|1|F|U|21 B=3NVI|1|F|U|5
  5 Basepair    21    5 UU cWW 
No need to probe because of interaction between a=3NVI|1|F|G|22 B=3NVI|1|F|C|4
  6 Basepair    22    4 GC cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G15 - C8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CGG'
           RightLetter: 'A'
               Comment: ' // Cluster node 3NVI|1|F|C|16:3NVI|1|F|G|19 and 3NVI|1|F|A|7:3NVI|1|F|A|7'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2500

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A20 - G6 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U21 - U5 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G22 - C4 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_69229.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.8603
   -8.1011
   -8.1011
   -7.8603
   -7.8603
  -10.0076
  -12.8561
  -11.2652

Timestamp 18-Jul-2025 22:48:37
pMakeSCFGModels: Making JAR3D model for motif group IL_69271.3, number 284 of 411
pMakeNodes starting loop:     a=5BTP|1|B|C|15 B=5BTP|1|B|G|41
  2 Basepair    15   41 CG cWW 
No need to probe because of interaction between a=5BTP|1|B|U|16 B=5BTP|1|B|U|40
  3 Basepair    16   40 UU cWW 
pMakeNodes probe for inserts:  a=5BTP|1|B|G|17 B=5BTP|1|B|A|39
    Insertion on left  5BTP|1|B|G|17
    Insertion on left  5BTP|1|B|A|18
    Insertion on left  5BTP|1|B|C|19
    Insertion on left  5BTP|1|B|G|20
    Insertion on left  5BTP|1|B|G|21
    Insertion on right 5BTP|1|B|A|39
pMakeNodesProbeForInsertions:  a 5BTP|1|B|G|25 interacts with 5BTP|1|B|C|38
pMakeNodesProbeForInsertions:  B 5BTP|1|B|C|38 interacts with 5BTP|1|B|G|25
pMakeNodesProbeForInsertions:  B 5BTP|1|B|C|38 interacts with 5BTP|1|B|G|25
pMakeNodes probed for insert:  a=5BTP|1|B|G|25 B=5BTP|1|B|C|38
  4 Basepair    25   38 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5BTP|1|B|G|17
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5BTP|1|B|A|18
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5BTP|1|B|C|19
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5BTP|1|B|G|20
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5BTP|1|B|G|21
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5BTP|1|B|C|24
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C15 - G41 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGACGG'
           RightLetter: 'AU'
               Comment: ' // Basepair U16 - U40 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5BTP|1|B|G|17'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5BTP|1|B|A|18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5BTP|1|B|C|19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5BTP|1|B|G|20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5BTP|1|B|G|21'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5BTP|1|B|C|24'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G25 - C38 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  15   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  16  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  17   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a hairpin at node 17

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_69271.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.4563
   -7.9158

Timestamp 18-Jul-2025 22:48:37
pMakeSCFGModels: Making JAR3D model for motif group IL_69440.3, number 285 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|343 B=5J7L|1|DA|G|295
  2 Basepair   343  295 CG cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|344 B=5J7L|1|DA|A|294
    Insertion on left  5J7L|1|DA|A|344
    Insertion on right 5J7L|1|DA|A|294
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|A|345 interacts with 5J7L|1|DA|A|346
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|U|293 interacts with 5J7L|1|DA|A|347
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|U|293 interacts with 5J7L|1|DA|A|347
pMakeNodes probed for insert:  a=5J7L|1|DA|A|345 B=5J7L|1|DA|U|293
pMakeNodes making a cluster near strand break a=5J7L|1|DA|A|345 B=5J7L|1|DA|U|293
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 5 and then 6 to 6
aa is 5 bb is 6
  3 Cluster   5J7L|1|DA|A|345:5J7L|1|DA|A|347 5J7L|1|DA|U|293:5J7L|1|DA|U|293
    LR Inter  5J7L|1|DA|A|347 5J7L|1|DA|U|293 cWW 
    LL Inter  5J7L|1|DA|A|345 5J7L|1|DA|A|346 cSH 
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Cluster Left  3  4  5 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|294
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|A|346
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: 'AG'
               Comment: ' // Basepair C343 - G295 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|294'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|A|346'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [3 4 5]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAA'
           RightLetter: 'U'
               Comment: ' // Cluster node 5J7L|1|DA|A|345:5J7L|1|DA|A|347 and 5J7L|1|DA|U|293:5J7L|1|DA|U|293'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   7   Cluster Left  3  4  5 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pUpdateModelWithSSF: IL_69440.3 allow insertions from initial node 8?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_69440.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.4385
   -4.9277
   -4.9277

Timestamp 18-Jul-2025 22:48:37
pMakeSCFGModels: Making JAR3D model for motif group IL_69543.3, number 286 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|C|1711 B=8P9A|1|AR|G|1733
  2 Basepair  1711 1733 CG cWW 
No need to probe because of interaction between a=8P9A|1|AR|G|1712 B=8P9A|1|AR|U|1732
  3 Basepair  1712 1732 GU tSH 
No need to probe because of interaction between a=8P9A|1|AR|G|1713 B=8P9A|1|AR|A|1731
  4 Basepair  1713 1731 GA tSH 
No need to probe because of interaction between a=8P9A|1|AR|A|1714 B=8P9A|1|AR|G|1730
pMakeNodes making a cluster near strand break a=8P9A|1|AR|A|1714 B=8P9A|1|AR|G|1730
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 6 and then 7 to 9
aa is 6 bb is 7
  5 Cluster   8P9A|1|AR|A|1714:8P9A|1|AR|U|1717 8P9A|1|AR|G|1727:8P9A|1|AR|G|1730
    LR Inter  8P9A|1|AR|A|1714 8P9A|1|AR|G|1727 tSS 
    LR Inter  8P9A|1|AR|U|1717 8P9A|1|AR|G|1727 cWW 
    LR Inter  8P9A|1|AR|A|1714 8P9A|1|AR|G|1730 tHS 
    Left  strand conserved insertion 8P9A|1|AR|A|1715 at position 2
    Right strand conserved insertion 8P9A|1|AR|G|1728 at position 2
pMakeNodesCluster a=7 B=6 at the end
pMakeNodesCluster a=7 B=6 at the end
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5   Cluster Left  4  5  6 Right  7  8  9
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1711 - G1733 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1712 - U1732 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1713 - A1731 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [4 5 6]
            RightIndex: [7 8 9]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AAU'
           RightLetter: 'GGG'
               Comment: ' // Cluster node 8P9A|1|AR|A|1714:8P9A|1|AR|U|1717 and 8P9A|1|AR|G|1727:8P9A|1|AR|G|1730'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: 2
              NormCons: 0.1009

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5   Cluster Left  4  5  6 Right  7  8  9
pMakeMotifModelFromSSF:   6   Initial Left  7 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 7
pUpdateModelWithSSF: IL_69543.3 allow insertions from initial node 6?
ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9940    0.0060    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_69543.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3002
   -8.5275
  -12.2321

Timestamp 18-Jul-2025 22:48:37
pMakeSCFGModels: Making JAR3D model for motif group IL_69986.1, number 287 of 411
pMakeNodes starting loop:     a=3D0M|1|X|U|7||||16_545 B=3D0M|1|X|A|12
  2 Basepair     7   12 UA cWW 
No need to probe because of interaction between a=3D0M|1|X|G|8||||16_545 B=3D0M|1|X|G|11
  3 Basepair     8   11 GG cHW 
No need to probe because of interaction between a=3D0M|1|X|A|9||||16_545 B=3D0M|1|X|U|10
  4 Basepair     9   10 AU cWW 
No need to probe because of interaction between a=3D0M|1|X|U|10||||16_545 B=3D0M|1|X|A|9
  5 Basepair    10    9 UA cWW 
No need to probe because of interaction between a=3D0M|1|X|G|11||||16_545 B=3D0M|1|X|G|8
  6 Basepair    11    8 GG cWH 
No need to probe because of interaction between a=3D0M|1|X|A|12||||16_545 B=3D0M|1|X|U|7
  7 Basepair    12    7 AU cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U7 - A12 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G8 - G11 cHW '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A9 - U10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U10 - A9 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G11 - G8 cWH '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A12 - U7 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 8
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 1 of 1, pair 2,11 for nucleotide 2 (G) making self BPh with edge 1
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_69986.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.6940

Timestamp 18-Jul-2025 22:48:38
pMakeSCFGModels: Making JAR3D model for motif group IL_70096.1, number 288 of 411
pMakeNodes starting loop:     a=6MWN|1|B|U|604 B=6MWN|1|B|G|675
  2 Basepair   604  675 UG cWW 
pMakeNodes probe for inserts:  a=6MWN|1|B|U|605 B=6MWN|1|B|U|671
    Insertion on left  6MWN|1|B|U|605
pMakeNodesProbeForInsertions:  a 6MWN|1|B|U|606 interacts with 6MWN|1|B|U|671
pMakeNodesProbeForInsertions:  B 6MWN|1|B|U|671 interacts with 6MWN|1|B|U|606
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6MWN|1|B|U|671 interacts with 6MWN|1|B|U|606
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6MWN|1|B|U|606 B=6MWN|1|B|U|671
  3 Basepair   606  671 UU cWW 
No need to probe because of interaction between a=6MWN|1|B|G|607 B=6MWN|1|B|C|670
  4 Basepair   607  670 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6MWN|1|B|U|605
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UU'
           RightLetter: 'G'
               Comment: ' // Basepair U604 - G675 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6MWN|1|B|U|605'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U606 - U671 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G607 - C670 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_70096.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8273

Timestamp 18-Jul-2025 22:48:38
pMakeSCFGModels: Making JAR3D model for motif group IL_70335.1, number 289 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|U|2611 B=9DFE|1|1A|A|2057
  2 Basepair  2611 2057 UA cWW 
pMakeNodes probe for inserts:  a=9DFE|1|1A|C|2612 B=9DFE|1|1A|G|2056
    Insertion on left  9DFE|1|1A|C|2612
    Insertion on left  9DFE|1|1A|U|2613
    Insertion on right 9DFE|1|1A|G|2056
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|U|2615 interacts with 9DFE|1|1A|A|2054
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|A|2054 interacts with 9DFE|1|1A|U|2615
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|A|2054 interacts with 9DFE|1|1A|U|2615
pMakeNodes probed for insert:  a=9DFE|1|1A|U|2615 B=9DFE|1|1A|A|2054
  3 Basepair  2615 2054 UA cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|C|2055
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|G|2056
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 9DFE|1|1A|C|2612
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UCU'
           RightLetter: 'GA'
               Comment: ' // Basepair U2611 - A2057 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|C|2055'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|G|2056'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 9DFE|1|1A|C|2612'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U2615 - A2054 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_70335.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.4816
   -5.4816

Timestamp 18-Jul-2025 22:48:38
pMakeSCFGModels: Making JAR3D model for motif group IL_70376.1, number 290 of 411
pMakeNodes starting loop:     a=8CRE|1|1|U|248 B=8CRE|1|1|G|169
  2 Basepair   248  169 UG cWW 
pMakeNodes probe for inserts:  a=8CRE|1|1|G|249 B=8CRE|1|1|U|168
    Insertion on left  8CRE|1|1|G|249
    Insertion on left  8CRE|1|1|G|251
pMakeNodesProbeForInsertions:  a 8CRE|1|1|A|253 interacts with 8CRE|1|1|U|168
pMakeNodesProbeForInsertions:  B 8CRE|1|1|U|168 interacts with 8CRE|1|1|A|253
pMakeNodesProbeForInsertions:  B 8CRE|1|1|U|168 interacts with 8CRE|1|1|A|253
pMakeNodes probed for insert:  a=8CRE|1|1|A|253 B=8CRE|1|1|U|168
  3 Basepair   253  168 AU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|G|169
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|U|248
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGG'
           RightLetter: 'G'
               Comment: ' // Basepair U248 - G169 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|G|169'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|U|248'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A253 - U168 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_70376.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.1466

Timestamp 18-Jul-2025 22:48:38
pMakeSCFGModels: Making JAR3D model for motif group IL_70411.2, number 291 of 411
pMakeNodes starting loop:     a=8CRE|1|1|U|3297 B=8CRE|1|1|G|3336
  2 Basepair  3297 3336 UG cWW 
No need to probe because of interaction between a=8CRE|1|1|G|3298 B=8CRE|1|1|A|3335
  3 Basepair  3298 3335 GA tSH 
pMakeNodes probe for inserts:  a=8CRE|1|1|U|3299 B=8CRE|1|1|U|3333
    Insertion on left  8CRE|1|1|U|3299
    Insertion on left  8CRE|1|1|A|3300
pMakeNodesProbeForInsertions:  a 8CRE|1|1|A|3301 interacts with 8CRE|1|1|U|3333
pMakeNodesProbeForInsertions:  B 8CRE|1|1|U|3333 interacts with 8CRE|1|1|A|3301
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8CRE|1|1|U|3333 interacts with 8CRE|1|1|A|3301
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8CRE|1|1|A|3301 B=8CRE|1|1|U|3333
  4 Basepair  3301 3333 AU tHH 
No need to probe because of interaction between a=8CRE|1|1|G|3302 B=8CRE|1|1|C|3332
  5 Basepair  3302 3332 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|U|3299
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|A|3300
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U3297 - G3336 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUA'
           RightLetter: 'A'
               Comment: ' // Basepair G3298 - A3335 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|U|3299'
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|A|3300'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A3301 - U3333 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G3302 - C3332 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  10   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_70411.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4620
   -6.4620
   -8.4578
   -8.6368
   -8.0578
   -5.4889
   -5.4889

Timestamp 18-Jul-2025 22:48:38
pMakeSCFGModels: Making JAR3D model for motif group IL_70627.3, number 292 of 411
pMakeNodes starting loop:     a=4GXY|1|A|G|148 B=4GXY|1|A|C|80
  2 Basepair   148   80 GC cWW 
pMakeNodes probe for inserts:  a=4GXY|1|A|G|149 B=4GXY|1|A|G|78
    Insertion on left  4GXY|1|A|G|149
    Insertion on right 4GXY|1|A|G|78
pMakeNodesProbeForInsertions:  a 4GXY|1|A|A|150 interacts with 4GXY|1|A|U|77
pMakeNodesProbeForInsertions:  B 4GXY|1|A|U|77 interacts with 4GXY|1|A|A|150
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4GXY|1|A|U|77 interacts with 4GXY|1|A|A|150
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4GXY|1|A|A|150 B=4GXY|1|A|U|77
  3 Basepair   150   77 AU tHW 
pMakeNodes probe for inserts:  a=4GXY|1|A|G|151 B=4GXY|1|A|G|76
    Insertion on left  4GXY|1|A|G|151
    Insertion on left  4GXY|1|A|U|152
pMakeNodesProbeForInsertions:  a 4GXY|1|A|C|153 interacts with 4GXY|1|A|G|76
pMakeNodesProbeForInsertions:  B 4GXY|1|A|G|76 interacts with 4GXY|1|A|C|153
pMakeNodesProbeForInsertions:  B 4GXY|1|A|G|76 interacts with 4GXY|1|A|C|153
pMakeNodes probed for insert:  a=4GXY|1|A|C|153 B=4GXY|1|A|G|76
  4 Basepair   153   76 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4GXY|1|A|U|77
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4GXY|1|A|G|151
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4GXY|1|A|A|79
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4GXY|1|A|C|80
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: 'GC'
               Comment: ' // Basepair G148 - C80 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4GXY|1|A|U|77'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4GXY|1|A|G|151'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AGU'
           RightLetter: 'U'
               Comment: ' // Basepair A150 - U77 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4GXY|1|A|A|79'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4GXY|1|A|C|80'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C153 - G76 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   8     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  7
pMakeMotifModelFromSSF:  10     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  11   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  12  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  13   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_70627.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8722
   -6.7308
   -9.3553

Timestamp 18-Jul-2025 22:48:38
pMakeSCFGModels: Making JAR3D model for motif group IL_70670.1, number 293 of 411
pMakeNodes starting loop:     a=4LCK|1|F|G|15 B=4LCK|1|F|C|91
  2 Basepair    15   91 GC cWW 
pMakeNodes probe for inserts:  a=4LCK|1|F|A|16 B=4LCK|1|F|A|90
    Insertion on left  4LCK|1|F|A|16
    Insertion on left  4LCK|1|F|A|17
    Insertion on left  4LCK|1|F|G|18
    Insertion on right 4LCK|1|F|A|90
    Insertion on right 4LCK|1|F|C|89
    Insertion on right 4LCK|1|F|G|88
    Insertion on right 4LCK|1|F|G|87
pMakeNodesProbeForInsertions:  a 4LCK|1|F|A|19 interacts with 4LCK|1|F|A|86
pMakeNodesProbeForInsertions:  B 4LCK|1|F|A|86 interacts with 4LCK|1|F|A|19
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4LCK|1|F|A|86 interacts with 4LCK|1|F|A|19
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4LCK|1|F|A|19 B=4LCK|1|F|A|86
  3 Basepair    19   86 AA tHH 
pMakeNodes probe for inserts:  a=4LCK|1|F|G|20 B=4LCK|1|F|A|85
pMakeNodesProbeForInsertions:  a 4LCK|1|F|G|20 interacts with 4LCK|1|F|U|21
pMakeNodesProbeForInsertions:  B 4LCK|1|F|A|85 interacts with 4LCK|1|F|U|21
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4LCK|1|F|A|85 interacts with 4LCK|1|F|U|21
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4LCK|1|F|G|20 B=4LCK|1|F|A|85
pMakeNodes making a cluster near strand break a=4LCK|1|F|G|20 B=4LCK|1|F|A|85
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 6 to 7 and then 12 to 12
aa is 7 bb is 12
  4 Cluster   4LCK|1|F|G|20:4LCK|1|F|U|21 4LCK|1|F|A|85:4LCK|1|F|A|85
    LR Inter  4LCK|1|F|U|21 4LCK|1|F|A|85 tWH 
    LL Inter  4LCK|1|F|G|20 4LCK|1|F|U|21 cSH 
pMakeNodesCluster a=8 B=11 at the end
pMakeNodesCluster a=8 B=11 at the end
No need to probe because of interaction between a=4LCK|1|F|A|22 B=4LCK|1|F|G|84
  5 Basepair    22   84 AG tHS 
No need to probe because of interaction between a=4LCK|1|F|U|23 B=4LCK|1|F|A|83
  6 Basepair    23   83 UA cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right 13
pMakeMotifModelFromSSF:   4   Cluster Left  6  7 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:   6  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   7   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LCK|1|F|A|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LCK|1|F|A|17
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LCK|1|F|G|18
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LCK|1|F|A|90
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LCK|1|F|C|89
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LCK|1|F|G|88
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LCK|1|F|G|87
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAAG'
           RightLetter: 'GGCAC'
               Comment: ' // Basepair G15 - C91 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LCK|1|F|A|16'
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LCK|1|F|A|17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LCK|1|F|G|18'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LCK|1|F|A|90'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LCK|1|F|C|89'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LCK|1|F|G|88'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 5
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LCK|1|F|G|87'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A19 - A86 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 19
             LeftIndex: [6 7]
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 4LCK|1|F|G|20:4LCK|1|F|U|21 and 4LCK|1|F|A|85:4LCK|1|F|A|85'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 21
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A22 - G84 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U23 - A83 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 18
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 17
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 17
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 17
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 17
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 17
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 17
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 17
pMakeMotifModelFromSSF:  10   Initial Left  5 Right 16
pMakeMotifModelFromSSF:  11     Fixed Left  5 Right 16
pMakeMotifModelFromSSF:  12   Initial Left  5 Right 15
pMakeMotifModelFromSSF:  13     Fixed Left  5 Right 15
pMakeMotifModelFromSSF:  14   Initial Left  5 Right 14
pMakeMotifModelFromSSF:  15     Fixed Left  5 Right 14
pMakeMotifModelFromSSF:  16   Initial Left  5 Right 13
pMakeMotifModelFromSSF:  17  Basepair Left  5 Right 13
pMakeMotifModelFromSSF:  18   Cluster Left  6  7 Right 12
pMakeMotifModelFromSSF:  19   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  20  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  21  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  22   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Found a hairpin at node 22

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_70670.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.3312

Timestamp 18-Jul-2025 22:48:39
pMakeSCFGModels: Making JAR3D model for motif group IL_70801.1, number 294 of 411
pMakeNodes starting loop:     a=5J7L|1|AA|C|477 B=5J7L|1|AA|G|455
  2 Basepair   477  455 CG cWW 
No need to probe because of interaction between a=5J7L|1|AA|A|478 B=5J7L|1|AA|G|454
  3 Basepair   478  454 AG cWW 
No need to probe because of interaction between a=5J7L|1|AA|U|479 B=5J7L|1|AA|G|453
  4 Basepair   479  453 UG cWW 
No need to probe because of interaction between a=5J7L|1|AA|U|480 B=5J7L|1|AA|A|452
  5 Basepair   480  452 UA tWW 
pMakeNodes probe for inserts:  a=5J7L|1|AA|G|481 B=5J7L|1|AA|A|451
    Insertion on left  5J7L|1|AA|G|481
    Insertion on left  5J7L|1|AA|A|482
    Insertion on right 5J7L|1|AA|A|451
pMakeNodesProbeForInsertions:  a 5J7L|1|AA|C|483 interacts with 5J7L|1|AA|G|450
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|G|450 interacts with 5J7L|1|AA|C|483
pMakeNodesProbeForInsertions:  B 5J7L|1|AA|G|450 interacts with 5J7L|1|AA|C|483
pMakeNodes probed for insert:  a=5J7L|1|AA|C|483 B=5J7L|1|AA|G|450
  6 Basepair   483  450 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|G|454
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|AA|G|455
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|AA|U|479
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C477 - G455 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A478 - G454 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U479 - G453 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGA'
           RightLetter: 'AA'
               Comment: ' // Basepair U480 - A452 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|G|454'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|AA|G|455'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|AA|U|479'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C483 - G450 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 10
pMakeMotifModelFromSSF:   6     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:   7   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   8     Fixed Left  6 Right  9
pMakeMotifModelFromSSF:   9   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  10     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  11   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  12  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  13   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_70801.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8858

Timestamp 18-Jul-2025 22:48:39
pMakeSCFGModels: Making JAR3D model for motif group IL_70923.9, number 295 of 411
pMakeNodes starting loop:     a=5G4T|1|A|C|3 B=5G4T|1|B|G|17
  2 Basepair     3   17 CG cWW 
No need to probe because of interaction between a=5G4T|1|A|G|4 B=5G4T|1|B|A|16
pMakeNodes making a cluster near strand break a=5G4T|1|A|G|4 B=5G4T|1|B|A|16
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 11 to 11
aa is 4 bb is 11
  3 Cluster   5G4T|1|A|G|4:5G4T|1|A|G|7 5G4T|1|B|A|16:5G4T|1|B|A|16
    LR Inter  5G4T|1|A|G|4 5G4T|1|B|A|16 tSS 
    LR Inter  5G4T|1|A|G|7 5G4T|1|B|A|16 tSH 
    Left  strand conserved insertion 5G4T|1|A|A|5 at position 2
pMakeNodesCluster a=5 B=10 at the end
pMakeNodesCluster a=5 B=10 at the end
No need to probe because of interaction between a=5G4T|1|A|A|8 B=5G4T|1|B|G|15
  4 Basepair     8   15 AG tHS 
No need to probe because of interaction between a=5G4T|1|A|A|9 B=5G4T|1|B|G|14
  5 Basepair     9   14 AG tHS 
No need to probe because of interaction between a=5G4T|1|A|C|10 B=5G4T|1|B|G|13
  6 Basepair    10   13 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C3 - G17 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4]
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GAG'
           RightLetter: 'A'
               Comment: ' // Cluster node 5G4T|1|A|G|4:5G4T|1|A|G|7 and 5G4T|1|B|A|16:5G4T|1|B|A|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.1817

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A8 - G15 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A9 - G14 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C10 - G13 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   8   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_70923.9_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.4957
   -5.4957
   -5.4957
   -5.4957
  -10.4335
   -9.7798
   -5.4957
   -6.1767
   -5.4957
   -5.4957
   -5.4957
  -13.2210
   -8.1829
   -5.4957
   -6.5173
   -8.7676
   -5.4957
   -8.1829
   -5.4957
   -7.5293
   -7.9919
   -5.4957
   -8.8441
  -11.9202
   -9.6203
   -9.6203
   -9.9982

Timestamp 18-Jul-2025 22:48:40
pMakeSCFGModels: Making JAR3D model for motif group IL_71294.3, number 296 of 411
pMakeNodes starting loop:     a=1L9A|1|B|C|190 B=1L9A|1|B|G|209
  2 Basepair   190  209 CG cWW 
No need to probe because of interaction between a=1L9A|1|B|C|191 B=1L9A|1|B|A|208
  3 Basepair   191  208 CA bif 
No need to probe because of interaction between a=1L9A|1|B|A|192 B=1L9A|1|B|C|207
  4 Basepair   192  207 AC tHW 
pMakeNodes probe for inserts:  a=1L9A|1|B|G|193 B=1L9A|1|B|G|206
    Insertion on left  1L9A|1|B|G|193
    Insertion on right 1L9A|1|B|G|206
pMakeNodesProbeForInsertions:  a 1L9A|1|B|G|194 interacts with 1L9A|1|B|A|205
pMakeNodesProbeForInsertions:  B 1L9A|1|B|A|205 interacts with 1L9A|1|B|G|194
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 1L9A|1|B|A|205 interacts with 1L9A|1|B|G|194
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=1L9A|1|B|G|194 B=1L9A|1|B|A|205
  5 Basepair   194  205 GA cWW 
No need to probe because of interaction between a=1L9A|1|B|U|195 B=1L9A|1|B|G|204
  6 Basepair   195  204 UG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1L9A|1|B|G|193
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1L9A|1|B|G|206
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C190 - G209 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C191 - A208 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: 'GC'
               Comment: ' // Basepair A192 - C207 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1L9A|1|B|G|193'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1L9A|1|B|G|206'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G194 - A205 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U195 - G204 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_71294.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.9291
  -11.5269

Timestamp 18-Jul-2025 22:48:40
pMakeSCFGModels: Making JAR3D model for motif group IL_71598.1, number 297 of 411
pMakeNodes starting loop:     a=6D3P|1|A|G|32 B=6D3P|1|A|C|9
  2 Basepair    32    9 GC cWW 
No need to probe because of interaction between a=6D3P|1|A|G|33 B=6D3P|1|A|A|8
  3 Basepair    33    8 GA tSH 
pMakeNodes probe for inserts:  a=6D3P|1|A|A|34 B=6D3P|1|A|U|6
    Insertion on left  6D3P|1|A|A|34
    Insertion on left  6D3P|1|A|A|35
pMakeNodesProbeForInsertions:  a 6D3P|1|A|A|36 interacts with 6D3P|1|A|U|6
pMakeNodesProbeForInsertions:  B 6D3P|1|A|U|6 interacts with 6D3P|1|A|A|36
pMakeNodesProbeForInsertions:  B 6D3P|1|A|U|6 interacts with 6D3P|1|A|A|36
pMakeNodes probed for insert:  a=6D3P|1|A|A|36 B=6D3P|1|A|U|6
  4 Basepair    36    6 AU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6D3P|1|A|A|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6D3P|1|A|C|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G32 - C9 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAA'
           RightLetter: 'A'
               Comment: ' // Basepair G33 - A8 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6D3P|1|A|A|8'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6D3P|1|A|C|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A36 - U6 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_71598.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.2181

Timestamp 18-Jul-2025 22:48:40
pMakeSCFGModels: Making JAR3D model for motif group IL_73002.1, number 298 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|U|675 B=8P9A|1|sR|G|655
  2 Basepair   675  655 UG cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|G|676 B=8P9A|1|sR|C|654
    Insertion on left  8P9A|1|sR|G|676
    Insertion on left  8P9A|1|sR|G|677
    Insertion on left  8P9A|1|sR|A|678
    Insertion on left  8P9A|1|sR|U|679
    Insertion on left  8P9A|1|sR|U|680
    Insertion on left  8P9A|1|sR|C|682
    Insertion on left  8P9A|1|sR|C|683
    Insertion on left  8P9A|1|sR|A|684
    Insertion on right 8P9A|1|sR|C|654
    Insertion on right 8P9A|1|sR|C|653
    Insertion on right 8P9A|1|sR|G|652
    Insertion on right 8P9A|1|sR|U|650
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|A|685 interacts with 8P9A|1|sR|U|649
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|649 interacts with 8P9A|1|sR|A|685
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|U|649 interacts with 8P9A|1|sR|A|685
pMakeNodes probed for insert:  a=8P9A|1|sR|A|685 B=8P9A|1|sR|U|649
  3 Basepair   685  649 AU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   4   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|U|650
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|G|651
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|G|652
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|C|653
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|C|654
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|G|655
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|U|675
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|G|676
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|C|682
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|U|681
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|U|680
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|U|679
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGGAUUCCA'
           RightLetter: 'UGCCG'
               Comment: ' // Basepair U675 - G655 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|U|650'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|G|651'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|G|652'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|C|653'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|C|654'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|G|655'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|U|675'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|G|676'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|C|682'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 10
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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                  lpar: []
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Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             LeftIndex: 10
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|U|681'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                  lpar: []
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Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|U|680'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 10
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 26
             LeftIndex: 10
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|U|679'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 28
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A685 - U649 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 30
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 15
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 15
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 15
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 15
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 15
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 15
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 15
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 15
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 15
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 15
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 15
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 15
pMakeMotifModelFromSSF:  18   Initial Left 10 Right 15
pMakeMotifModelFromSSF:  19     Fixed Left 10 Right 15
pMakeMotifModelFromSSF:  20   Initial Left 10 Right 14
pMakeMotifModelFromSSF:  21     Fixed Left 10 Right 14
pMakeMotifModelFromSSF:  22   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  23     Fixed Left 10 Right 13
pMakeMotifModelFromSSF:  24   Initial Left 10 Right 12
pMakeMotifModelFromSSF:  25     Fixed Left 10 Right 12
pMakeMotifModelFromSSF:  26   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  27  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  28   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 28
pNextNodeJunction: Found a hairpin at node 28

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_73002.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.2297

Timestamp 18-Jul-2025 22:48:40
pMakeSCFGModels: Making JAR3D model for motif group IL_73355.1, number 299 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|C|2098 B=8P9A|1|AR|G|1948
  2 Basepair  2098 1948 CG cWW 
pMakeNodes probe for inserts:  a=8P9A|1|AR|A|2099 B=8P9A|1|AR|G|1947
    Insertion on left  8P9A|1|AR|A|2099
    Insertion on left  8P9A|1|AR|A|2100
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|C|2101 interacts with 8P9A|1|AR|G|1947
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|G|1947 interacts with 8P9A|1|AR|C|2101
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|G|1947 interacts with 8P9A|1|AR|C|2101
pMakeNodes probed for insert:  a=8P9A|1|AR|C|2101 B=8P9A|1|AR|G|1947
  3 Basepair  2101 1947 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|G|1948
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|C|2098
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAA'
           RightLetter: 'G'
               Comment: ' // Basepair C2098 - G1948 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|G|1948'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|C|2098'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2101 - G1947 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_73355.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.9345
   -3.9345

Timestamp 18-Jul-2025 22:48:40
pMakeSCFGModels: Making JAR3D model for motif group IL_73452.2, number 300 of 411
pMakeNodes starting loop:     a=8S95|1|C|C|78 B=8S95|1|C|G|109
  2 Basepair    78  109 CG cWW 
pMakeNodes probe for inserts:  a=8S95|1|C|A|80 B=8S95|1|C|C|108
    Insertion on left  8S95|1|C|A|80
pMakeNodesProbeForInsertions:  a 8S95|1|C|G|81 interacts with 8S95|1|C|C|108
pMakeNodesProbeForInsertions:  B 8S95|1|C|C|108 interacts with 8S95|1|C|G|81
pMakeNodesProbeForInsertions:  B 8S95|1|C|C|108 interacts with 8S95|1|C|G|81
pMakeNodes probed for insert:  a=8S95|1|C|G|81 B=8S95|1|C|C|108
  3 Basepair    81  108 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8S95|1|C|U|79
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CA'
           RightLetter: 'G'
               Comment: ' // Basepair C78 - G109 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8S95|1|C|U|79'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G81 - C108 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_73452.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.5729
   -5.7716
   -6.8814

Timestamp 18-Jul-2025 22:48:40
pMakeSCFGModels: Making JAR3D model for motif group IL_73700.1, number 301 of 411
pMakeNodes starting loop:     a=6N5P|1|A|C|36 B=6N5P|1|A|G|99
  2 Basepair    36   99 CG cWW 
pMakeNodes probe for inserts:  a=6N5P|1|A|G|37 B=6N5P|1|A|A|98
    Insertion on left  6N5P|1|A|G|37
    Insertion on left  6N5P|1|A|C|38
    Insertion on left  6N5P|1|A|U|39
pMakeNodesProbeForInsertions:  a 6N5P|1|A|U|42 interacts with 6N5P|1|A|A|96
pMakeNodesProbeForInsertions:  B 6N5P|1|A|A|98 interacts with 6N5P|1|A|C|94
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 6N5P|1|A|A|98 interacts with 6N5P|1|A|C|94
pMakeNodes probed for insert:  a=6N5P|1|A|U|42 B=6N5P|1|A|A|98
pMakeNodes making a cluster near strand break a=6N5P|1|A|U|42 B=6N5P|1|A|A|98
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 7 and then 8 to 12
aa is 7 bb is 8
  3 Cluster   6N5P|1|A|U|42:6N5P|1|A|G|45 6N5P|1|A|C|94:6N5P|1|A|A|98
    LR Inter  6N5P|1|A|G|45 6N5P|1|A|C|94 cWW 
    LR Inter  6N5P|1|A|G|44 6N5P|1|A|G|95 tHS 
    LR Inter  6N5P|1|A|U|42 6N5P|1|A|A|96 cWW 
    LR Inter  6N5P|1|A|G|44 6N5P|1|A|C|97 cWW 
    RR Inter  6N5P|1|A|C|94 6N5P|1|A|A|98 tSW 
pMakeNodesCluster a=8 B=7 at the end
pMakeNodesCluster a=8 B=7 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  5  6  7 Right  8  9 10 11 12
pMakeMotifModelFromSSF:   4   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N5P|1|A|G|37
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N5P|1|A|C|38
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6N5P|1|A|U|39
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGCU'
           RightLetter: 'G'
               Comment: ' // Basepair C36 - G99 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6N5P|1|A|G|37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2 3 4 5]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0627

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6N5P|1|A|C|38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6N5P|1|A|U|39'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 10
             LeftIndex: [5 6 7]
            RightIndex: [8 9 10 11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UGG'
           RightLetter: 'CGACA'
               Comment: ' // Cluster node 6N5P|1|A|U|42:6N5P|1|A|G|45 and 6N5P|1|A|C|94:6N5P|1|A|A|98'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2 3 4 5]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0627

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9   Cluster Left  5  6  7 Right  8  9 10 11 12
pMakeMotifModelFromSSF:  10   Initial Left  8 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 11
pUpdateModelWithSSF: IL_73700.1 allow insertions from initial node 10?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_73700.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.0598

Timestamp 18-Jul-2025 22:48:41
pMakeSCFGModels: Making JAR3D model for motif group IL_73759.1, number 302 of 411
pMakeNodes starting loop:     a=7OAX|1|A|G|10 B=7OAX|1|A|C|44
pMakeNodes making a cluster near strand break a=7OAX|1|A|G|10 B=7OAX|1|A|C|44
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 9 to 9
aa is 2 bb is 9
  2 Cluster   7OAX|1|A|G|10:7OAX|1|A|A|11 7OAX|1|A|C|44:7OAX|1|A|C|44
    LR Inter  7OAX|1|A|G|10 7OAX|1|A|C|44 cWW 
    LR Inter  7OAX|1|A|A|11 7OAX|1|A|C|44 tHS 
    LL Inter  7OAX|1|A|G|10 7OAX|1|A|A|11 cSH 
pMakeNodesCluster a=3 B=8 at the end
pMakeNodesCluster a=3 B=8 at the end
No need to probe because of interaction between a=7OAX|1|A|G|12 B=7OAX|1|A|G|42
  3 Basepair    12   42 GG cWH 
No need to probe because of interaction between a=7OAX|1|A|G|13 B=7OAX|1|A|G|41
  4 Basepair    13   41 GG cHW 
No need to probe because of interaction between a=7OAX|1|A|G|15 B=7OAX|1|A|C|40
  5 Basepair    15   40 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GA'
           RightLetter: 'C'
               Comment: ' // Cluster node 7OAX|1|A|G|10:7OAX|1|A|A|11 and 7OAX|1|A|C|44:7OAX|1|A|C|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0119
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G12 - G42 cWH '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G13 - G41 cHW '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G15 - C40 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  9
pMakeMotifModelFromSSF:   3   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_73759.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.8710

Timestamp 18-Jul-2025 22:48:41
pMakeSCFGModels: Making JAR3D model for motif group IL_73789.1, number 303 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|C|374 B=8CRE|1|CM|G|363
  2 Basepair   374  363 CG cWW 
No need to probe because of interaction between a=8CRE|1|CM|G|375 B=8CRE|1|CM|G|362
  3 Basepair   375  362 GG tSH 
pMakeNodes probe for inserts:  a=8CRE|1|CM|A|376 B=8CRE|1|CM|G|361
    Insertion on left  8CRE|1|CM|A|376
    Insertion on left  8CRE|1|CM|U|377
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|C|379 interacts with 8CRE|1|CM|G|361
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|361 interacts with 8CRE|1|CM|C|379
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|361 interacts with 8CRE|1|CM|C|379
pMakeNodes probed for insert:  a=8CRE|1|CM|C|379 B=8CRE|1|CM|G|361
  4 Basepair   379  361 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|G|363
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|C|374
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C374 - G363 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAU'
           RightLetter: 'G'
               Comment: ' // Basepair G375 - G362 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|G|363'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|C|374'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C379 - G361 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_73789.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.3606
   -4.3606

Timestamp 18-Jul-2025 22:48:41
pMakeSCFGModels: Making JAR3D model for motif group IL_74051.1, number 304 of 411
pMakeNodes starting loop:     a=5XTM|1|B|C|16 B=5XTM|1|B|G|33
  2 Basepair    16   33 CG cWW 
No need to probe because of interaction between a=5XTM|1|B|G|17 B=5XTM|1|B|A|32
pMakeNodes making a cluster near strand break a=5XTM|1|B|G|17 B=5XTM|1|B|A|32
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 10 to 10
aa is 4 bb is 10
  3 Cluster   5XTM|1|B|G|17:5XTM|1|B|G|20 5XTM|1|B|A|32:5XTM|1|B|A|32
    LR Inter  5XTM|1|B|G|17 5XTM|1|B|A|32 tSS 
    LR Inter  5XTM|1|B|G|20 5XTM|1|B|A|32 tSH 
    Left  strand conserved insertion 5XTM|1|B|G|18 at position 2
pMakeNodesCluster a=5 B=9 at the end
pMakeNodesCluster a=5 B=9 at the end
No need to probe because of interaction between a=5XTM|1|B|A|21 B=5XTM|1|B|G|31
  4 Basepair    21   31 AG tHS 
pMakeNodes probe for inserts:  a=5XTM|1|B|A|22 B=5XTM|1|B|C|30
    Insertion on left  5XTM|1|B|A|22
pMakeNodesProbeForInsertions:  a 5XTM|1|B|G|23 interacts with 5XTM|1|B|C|30
pMakeNodesProbeForInsertions:  B 5XTM|1|B|C|30 interacts with 5XTM|1|B|G|23
pMakeNodesProbeForInsertions:  B 5XTM|1|B|C|30 interacts with 5XTM|1|B|G|23
pMakeNodes probed for insert:  a=5XTM|1|B|G|23 B=5XTM|1|B|C|30
  5 Basepair    23   30 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5XTM|1|B|A|21
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C16 - G33 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGG'
           RightLetter: 'A'
               Comment: ' // Cluster node 5XTM|1|B|G|17:5XTM|1|B|G|20 and 5XTM|1|B|A|32:5XTM|1|B|A|32'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.1817

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'G'
               Comment: ' // Basepair A21 - G31 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5XTM|1|B|A|21'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G23 - C30 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  9
pMakeMotifModelFromSSF:   6     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:   7   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_74051.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.7926
   -4.7926
   -4.7926

Timestamp 18-Jul-2025 22:48:41
pMakeSCFGModels: Making JAR3D model for motif group IL_74184.1, number 305 of 411
pMakeNodes starting loop:     a=4GXY|1|A|C|95 B=4GXY|1|A|G|130
  2 Basepair    95  130 CG cWW 
pMakeNodes probe for inserts:  a=4GXY|1|A|G|96 B=4GXY|1|A|G|129
    Insertion on left  4GXY|1|A|G|96
    Insertion on left  4GXY|1|A|G|97
    Insertion on left  4GXY|1|A|G|98
    Insertion on left  4GXY|1|A|A|99
    Insertion on left  4GXY|1|A|U|100
pMakeNodesProbeForInsertions:  a 4GXY|1|A|G|101 interacts with 4GXY|1|A|G|129
pMakeNodesProbeForInsertions:  B 4GXY|1|A|G|129 interacts with 4GXY|1|A|G|101
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4GXY|1|A|G|129 interacts with 4GXY|1|A|G|101
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4GXY|1|A|G|101 B=4GXY|1|A|G|129
  3 Basepair   101  129 GG tHS 
No need to probe because of interaction between a=4GXY|1|A|G|103 B=4GXY|1|A|C|128
  4 Basepair   103  128 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4GXY|1|A|G|96
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4GXY|1|A|G|97
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4GXY|1|A|G|98
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4GXY|1|A|A|99
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4GXY|1|A|U|100
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGGGAU'
           RightLetter: 'G'
               Comment: ' // Basepair C95 - G130 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4GXY|1|A|G|96'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4GXY|1|A|G|97'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4GXY|1|A|G|98'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4GXY|1|A|A|99'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4GXY|1|A|U|100'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G101 - G129 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G103 - C128 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  13  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  14  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  15   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a hairpin at node 15

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_74184.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2609

Timestamp 18-Jul-2025 22:48:41
pMakeSCFGModels: Making JAR3D model for motif group IL_74367.1, number 306 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|G|680 B=8P9A|1|AR|C|700
  2 Basepair   680  700 GC cWW 
pMakeNodes probe for inserts:  a=8P9A|1|AR|U|681 B=8P9A|1|AR|A|699
    Insertion on left  8P9A|1|AR|U|681
    Insertion on left  8P9A|1|AR|U|682
    Insertion on right 8P9A|1|AR|A|699
    Insertion on right 8P9A|1|AR|U|698
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|U|683 interacts with 8P9A|1|AR|A|697
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|A|697 interacts with 8P9A|1|AR|U|683
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|A|697 interacts with 8P9A|1|AR|U|683
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|AR|U|683 B=8P9A|1|AR|A|697
  3 Basepair   683  697 UA bif 
No need to probe because of interaction between a=8P9A|1|AR|G|684 B=8P9A|1|AR|C|696
  4 Basepair   684  696 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|U|681
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|U|682
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|A|699
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|U|698
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUU'
           RightLetter: 'UAC'
               Comment: ' // Basepair G680 - C700 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|U|681'
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|U|682'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|A|699'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|U|698'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U683 - A697 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G684 - C696 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  4 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:  12  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  13   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_74367.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.1614
   -5.2470

Timestamp 18-Jul-2025 22:48:41
pMakeSCFGModels: Making JAR3D model for motif group IL_74746.1, number 307 of 411
pMakeNodes starting loop:     a=3HJW|1|D|G|9 B=3HJW|1|D|C|46
  2 Basepair     9   46 GC cWW 
pMakeNodes probe for inserts:  a=3HJW|1|D|A|11 B=3HJW|1|D|C|45
    Insertion on left  3HJW|1|D|A|11
    Insertion on left  3HJW|1|D|A|12
    Insertion on left  3HJW|1|D|C|13
    Insertion on left  3HJW|1|D|C|14
    Insertion on left  3HJW|1|D|G|15
    Insertion on right 3HJW|1|D|C|45
    Insertion on right 3HJW|1|D|U|44
    Insertion on right 3HJW|1|D|C|43
    Insertion on right 3HJW|1|D|G|42
    Insertion on right 3HJW|1|D|C|41
pMakeNodesProbeForInsertions:  a 3HJW|1|D|C|16 interacts with 3HJW|1|D|U|40
pMakeNodesProbeForInsertions:  B 3HJW|1|D|U|40 interacts with 3HJW|1|D|C|16
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3HJW|1|D|U|40 interacts with 3HJW|1|D|C|16
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3HJW|1|D|C|16 B=3HJW|1|D|U|40
  3 Basepair    16   40 CU cWW 
No need to probe because of interaction between a=3HJW|1|D|G|17 B=3HJW|1|D|U|39
  4 Basepair    17   39 GU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3HJW|1|D|A|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3HJW|1|D|A|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3HJW|1|D|A|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3HJW|1|D|C|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3HJW|1|D|C|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3HJW|1|D|U|44
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3HJW|1|D|C|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3HJW|1|D|G|42
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3HJW|1|D|C|41
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3HJW|1|D|U|40
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAACCG'
           RightLetter: 'CGCUCC'
               Comment: ' // Basepair G9 - C46 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3HJW|1|D|A|10'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 5

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Node 6

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Node 7

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Node 8

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Node 9

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Node 10

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Node 11

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Node 12

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Node 13

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Node 14

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Node 15

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Node 16

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Node 17

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 18

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Node 19

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Node 20

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 21
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Node 21

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 22

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 23
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Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 15
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 15
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 15
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 15
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 15
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 15
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 15
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 15
pMakeMotifModelFromSSF:  14   Initial Left  7 Right 14
pMakeMotifModelFromSSF:  15     Fixed Left  7 Right 14
pMakeMotifModelFromSSF:  16   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  17     Fixed Left  7 Right 13
pMakeMotifModelFromSSF:  18   Initial Left  7 Right 12
pMakeMotifModelFromSSF:  19     Fixed Left  7 Right 12
pMakeMotifModelFromSSF:  20   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  21     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:  22   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  23  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  24  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  25   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Found a hairpin at node 25

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_74746.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -14.5056
  -14.9033

Timestamp 18-Jul-2025 22:48:42
pMakeSCFGModels: Making JAR3D model for motif group IL_74957.1, number 308 of 411
pMakeNodes starting loop:     a=2R8S|1|R|U|182 B=2R8S|1|R|A|136
  2 Basepair   182  136 UA cWW 
pMakeNodes probe for inserts:  a=2R8S|1|R|A|183 B=2R8S|1|R|U|135
    Insertion on left  2R8S|1|R|A|183
    Insertion on left  2R8S|1|R|A|184
pMakeNodesProbeForInsertions:  a 2R8S|1|R|A|187 interacts with 2R8S|1|R|U|135
pMakeNodesProbeForInsertions:  B 2R8S|1|R|U|135 interacts with 2R8S|1|R|A|187
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 2R8S|1|R|U|135 interacts with 2R8S|1|R|A|187
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=2R8S|1|R|A|187 B=2R8S|1|R|U|135
  3 Basepair   187  135 AU cHW 
pMakeNodes probe for inserts:  a=2R8S|1|R|G|188 B=2R8S|1|R|G|134
    Insertion on left  2R8S|1|R|G|188
pMakeNodesProbeForInsertions:  a 2R8S|1|R|C|189 interacts with 2R8S|1|R|G|134
pMakeNodesProbeForInsertions:  B 2R8S|1|R|G|134 interacts with 2R8S|1|R|C|189
pMakeNodesProbeForInsertions:  B 2R8S|1|R|G|134 interacts with 2R8S|1|R|C|189
pMakeNodes probed for insert:  a=2R8S|1|R|C|189 B=2R8S|1|R|G|134
  4 Basepair   189  134 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2R8S|1|R|U|135
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2R8S|1|R|A|136
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 2R8S|1|R|A|183
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UAA'
           RightLetter: 'A'
               Comment: ' // Basepair U182 - A136 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2R8S|1|R|U|135'
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2R8S|1|R|A|136'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AG'
           RightLetter: 'U'
               Comment: ' // Basepair A187 - U135 cHW '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 2R8S|1|R|A|183'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C189 - G134 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  11   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_74957.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.6461

Timestamp 18-Jul-2025 22:48:42
pMakeSCFGModels: Making JAR3D model for motif group IL_75283.2, number 309 of 411
pMakeNodes starting loop:     a=3U4M|1|B|C|2161 B=3U4M|1|B|G|2127
pMakeNodes making a cluster near strand break a=3U4M|1|B|C|2161 B=3U4M|1|B|G|2127
pMakeNodesCluster: amax is 14 bmin is 15, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 13 and then 16 to 18
aa is 13 bb is 16
  2 Cluster   3U4M|1|B|C|2161:3U4M|1|B|A|2173 3U4M|1|B|G|2125:3U4M|1|B|G|2127
    LR Inter  3U4M|1|B|A|2173 3U4M|1|B|G|2125 tHS 
    LR Inter  3U4M|1|B|C|2161 3U4M|1|B|G|2127 cWW 
    LR Inter  3U4M|1|B|A|2173 3U4M|1|B|G|2127 tSS 
    LL Inter  3U4M|1|B|U|2167 3U4M|1|B|A|2171 tWH 
    LL Inter  3U4M|1|B|G|2166 3U4M|1|B|U|2172 tWH 
    Left  strand conserved insertion 3U4M|1|B|G|2162 at position 2
    Left  strand conserved insertion 3U4M|1|B|C|2163 at position 3
    Left  strand conserved insertion 3U4M|1|B|C|2164 at position 4
    Left  strand conserved insertion 3U4M|1|B|G|2165 at position 5
    Left  strand conserved insertion 3U4M|1|B|G|2168 at position 8
    Left  strand conserved insertion 3U4M|1|B|A|2169 at position 9
    Left  strand conserved insertion 3U4M|1|B|A|2170 at position 10
    Right strand conserved insertion 3U4M|1|B|A|2126 at position 2
pMakeNodesCluster a=14 B=15 at the end
pMakeNodesCluster a=14 B=15 at the end
No need to probe because of interaction between a=3U4M|1|B|C|2174 B=3U4M|1|B|G|2124
  3 Basepair  2174 2124 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6  7  8  9 10 11 12 13 Right 16 17 18
pMakeMotifModelFromSSF:   3  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:   4   Hairpin Left 15 Right 14
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 18
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [18×18 double]
         Extensibility: [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5 6 7 8 9 10 11 12 13]
            RightIndex: [16 17 18]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CGCCGGUGAAAUA'
           RightLetter: 'GAG'
               Comment: ' // Cluster node 3U4M|1|B|C|2161:3U4M|1|B|A|2173 and 3U4M|1|B|G|2125:3U4M|1|B|G|2127'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×13 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8 9 10 11 12 13]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [13×2 double]
    InteractionComment: {1×13 cell}
      JunctionDeletion: []
          InterIndices: [13×2 double]
          LeftNotInter: [2 3 4 5 8 9 10]
         RightNotInter: 2
              NormCons: 0.0989
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 14
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 14
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2174 - G2124 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 15
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 15
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 18
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6  7  8  9 10 11 12 13 Right 16 17 18
pMakeMotifModelFromSSF:   3   Initial Left 14 Right 15
pMakeMotifModelFromSSF:   4  Basepair Left 14 Right 15
pMakeMotifModelFromSSF:   5   Hairpin Left 15 Right 14
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_75283.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7178
   -8.2502
   -6.7178

Timestamp 18-Jul-2025 22:48:42
pMakeSCFGModels: Making JAR3D model for motif group IL_75294.1, number 310 of 411
pMakeNodes starting loop:     a=9DFE|1|1A|C|2870 B=9DFE|1|1A|G|2846
  2 Basepair  2870 2846 CG cWW 
No need to probe because of interaction between a=9DFE|1|1A|C|2871 B=9DFE|1|1A|G|2845
  3 Basepair  2871 2845 CG bif 
pMakeNodes probe for inserts:  a=9DFE|1|1A|G|2872 B=9DFE|1|1A|G|2844
    Insertion on left  9DFE|1|1A|G|2872
    Insertion on left  9DFE|1|1A|A|2873
    Insertion on right 9DFE|1|1A|G|2844
pMakeNodesProbeForInsertions:  a 9DFE|1|1A|C|2874 interacts with 9DFE|1|1A|G|2843
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|G|2843 interacts with 9DFE|1|1A|C|2874
pMakeNodesProbeForInsertions:  B 9DFE|1|1A|G|2843 interacts with 9DFE|1|1A|C|2874
pMakeNodes probed for insert:  a=9DFE|1|1A|C|2874 B=9DFE|1|1A|G|2843
  4 Basepair  2874 2843 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|G|2845
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 9DFE|1|1A|G|2846
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 9DFE|1|1A|G|2872
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2870 - G2846 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGA'
           RightLetter: 'GG'
               Comment: ' // Basepair C2871 - G2845 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|G|2845'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 9DFE|1|1A|G|2846'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 9DFE|1|1A|G|2872'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2874 - G2843 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  11   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_75294.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.0311
   -7.9162

Timestamp 18-Jul-2025 22:48:42
pMakeSCFGModels: Making JAR3D model for motif group IL_76308.6, number 311 of 411
pMakeNodes starting loop:     a=1LNT|1|A|U|4 B=1LNT|1|B|G|21
  2 Basepair     4   21 UG cWW 
No need to probe because of interaction between a=1LNT|1|A|C|5 B=1LNT|1|B|A|20
  3 Basepair     5   20 CA tSH 
No need to probe because of interaction between a=1LNT|1|A|A|6 B=1LNT|1|B|C|19
  4 Basepair     6   19 AC tHW 
No need to probe because of interaction between a=1LNT|1|A|G|7 B=1LNT|1|B|G|18
  5 Basepair     7   18 GG tHS 
No need to probe because of interaction between a=1LNT|1|A|G|8 B=1LNT|1|B|A|17
  6 Basepair     8   17 GA cWW 
No need to probe because of interaction between a=1LNT|1|A|U|9 B=1LNT|1|B|A|16
  7 Basepair     9   16 UA cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U4 - G21 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C5 - A20 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A6 - C19 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G7 - G18 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G8 - A17 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U9 - A16 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_76308.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.4493
   -8.1049
   -7.4493
  -12.0486
  -14.9368

Timestamp 18-Jul-2025 22:48:42
pMakeSCFGModels: Making JAR3D model for motif group IL_76319.5, number 312 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|U|1257 B=8CRE|1|CM|G|1424
  2 Basepair  1257 1424 UG cWW 
pMakeNodes probe for inserts:  a=8CRE|1|CM|G|1258 B=8CRE|1|CM|U|1423
    Insertion on left  8CRE|1|CM|G|1258
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|A|1260 interacts with 8CRE|1|CM|U|1423
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|U|1423 interacts with 8CRE|1|CM|A|1260
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|U|1423 interacts with 8CRE|1|CM|A|1260
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8CRE|1|CM|A|1260 B=8CRE|1|CM|U|1423
  3 Basepair  1260 1423 AU cWS 
No need to probe because of interaction between a=8CRE|1|CM|U|1261 B=8CRE|1|CM|A|1422
  4 Basepair  1261 1422 UA cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|G|1258
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UG'
           RightLetter: 'G'
               Comment: ' // Basepair U1257 - G1424 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|G|1258'
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A1260 - U1423 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1261 - A1422 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   7   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_76319.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.7963
   -4.7963
   -4.7963

Timestamp 18-Jul-2025 22:48:43
pMakeSCFGModels: Making JAR3D model for motif group IL_76460.1, number 313 of 411
pMakeNodes starting loop:     a=6R47|1|A|C|28 B=6R47|1|B|G|63
  2 Basepair    28   63 CG cWW 
No need to probe because of interaction between a=6R47|1|A|U|29 B=6R47|1|B|U|62
  3 Basepair    29   62 UU cWW 
pMakeNodes probe for inserts:  a=6R47|1|A|C|30 B=6R47|1|B|G|61
    Insertion on left  6R47|1|A|C|30
    Insertion on left  6R47|1|A|A|31
    Insertion on left  6R47|1|A|G|32
pMakeNodesProbeForInsertions:  a 6R47|1|A|A|33 interacts with 6R47|1|A|C|41
pMakeNodesProbeForInsertions:  B 6R47|1|B|G|61 interacts with 6R47|1|A|G|42
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but a makes a more important one
pMakeNodesProbeForInsertions:  B 6R47|1|B|G|61 interacts with 6R47|1|A|G|42
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6R47|1|A|A|33 B=6R47|1|B|G|61
pMakeNodes making a cluster near strand break a=6R47|1|A|A|33 B=6R47|1|B|G|61
pMakeNodesCluster: amax is 17 bmin is 18, use_amax is 1
pMakeNodesCluster: Cluster goes from 6 to 15 and then 20 to 20
aa is 15 bb is 20
  4 Cluster   6R47|1|A|A|33:6R47|1|A|G|42 6R47|1|B|G|61:6R47|1|B|G|61
    LR Inter  6R47|1|A|G|42 6R47|1|B|G|61 tHS 
    LL Inter  6R47|1|A|A|33 6R47|1|A|C|41 cWW 
    Left  strand conserved insertion 6R47|1|A|C|34 at position 2
    Left  strand conserved insertion 6R47|1|A|C|35 at position 3
    Left  strand conserved insertion 6R47|1|A|CBV|36 at position 4
    Left  strand conserved insertion 6R47|1|A|G|37 at position 5
    Left  strand conserved insertion 6R47|1|A|A|38 at position 6
    Left  strand conserved insertion 6R47|1|A|A|39 at position 7
    Left  strand conserved insertion 6R47|1|A|G|40 at position 8
pMakeNodesCluster a=16 B=19 at the end
pMakeNodesCluster a=16 B=19 at the end
pMakeNodes probe for inserts:  a=6R47|1|A|U|43 B=6R47|1|B|G|60
    Insertion on left  6R47|1|A|U|43
    Insertion on right 6R47|1|B|G|60
pMakeNodesProbeForInsertions:  a 6R47|1|A|G|44 interacts with 6R47|1|B|C|59
pMakeNodesProbeForInsertions:  B 6R47|1|B|C|59 interacts with 6R47|1|A|G|44
pMakeNodesProbeForInsertions:  B 6R47|1|B|C|59 interacts with 6R47|1|A|G|44
  5 Initial     43 (1 insertion) and   60 (1 insertion)
pMakeNodes probed for insert:  a=6R47|1|A|G|44 B=6R47|1|B|C|59
  6 Basepair    44   59 GC cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 22
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 22
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 21
pMakeMotifModelFromSSF:   4   Cluster Left  6  7  8  9 10 11 12 13 14 15 Right 20
pMakeMotifModelFromSSF:   5   Initial Left 16 Right 19
pMakeMotifModelFromSSF:   6  Basepair Left 17 Right 18
pMakeMotifModelFromSSF:   7   Hairpin Left 18 Right 17
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6R47|1|A|C|30
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6R47|1|A|A|31
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6R47|1|A|G|32
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6R47|1|A|U|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6R47|1|B|G|60
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 22
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [22×22 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 22
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C28 - G63 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UCAG'
           RightLetter: 'U'
               Comment: ' // Basepair U29 - U62 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6R47|1|A|C|30'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×9 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8 9 10]
                 Right: 1
      InsertionComment: []
                IBases: [9×2 double]
    InteractionComment: {1×9 cell}
      JunctionDeletion: []
          InterIndices: [9×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4 5 6 7 8]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6R47|1|A|A|31'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 18
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6R47|1|A|G|32'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 11
             LeftIndex: [6 7 8 9 10 11 12 13 14 15]
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'ACCCGAAGCG'
           RightLetter: 'G'
               Comment: ' // Cluster node 6R47|1|A|A|33:6R47|1|A|G|42 and 6R47|1|B|G|61:6R47|1|B|G|61'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×9 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8 9 10]
                 Right: 1
      InsertionComment: []
                IBases: [9×2 double]
    InteractionComment: {1×9 cell}
      JunctionDeletion: []
          InterIndices: [9×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4 5 6 7 8]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 16
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Initial node 6R47|1|A|U|43 - 6R47|1|B|G|60 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 16
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6R47|1|A|U|43'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 17
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 17
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6R47|1|B|G|60'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 17
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 17
             LeftIndex: 17
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G44 - C59 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 19
             LeftIndex: 18
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 18
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 22
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 22
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 21
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 20
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 20
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 20
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 20
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 20
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 20
pMakeMotifModelFromSSF:  10   Cluster Left  6  7  8  9 10 11 12 13 14 15 Right 20
pMakeMotifModelFromSSF:  11   Initial Left 16 Right 19
pMakeMotifModelFromSSF:  12     Fixed Left 16 Right 19
pMakeMotifModelFromSSF:  13   Initial Left 17 Right 19
pMakeMotifModelFromSSF:  14     Fixed Left 17 Right 19
pMakeMotifModelFromSSF:  15   Initial Left 17 Right 18
pMakeMotifModelFromSSF:  16  Basepair Left 17 Right 18
pMakeMotifModelFromSSF:  17   Hairpin Left 18 Right 17
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a hairpin at node 17

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_76460.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -12.3350

Timestamp 18-Jul-2025 22:48:43
pMakeSCFGModels: Making JAR3D model for motif group IL_76709.2, number 314 of 411
pMakeNodes starting loop:     a=1MJI|1|D|G|51 B=1MJI|1|D|C|31
  2 Basepair    51   31 GC cWW 
pMakeNodes probe for inserts:  a=1MJI|1|D|A|52 B=1MJI|1|D|C|30
    Insertion on left  1MJI|1|D|A|52
    Insertion on left  1MJI|1|D|A|53
pMakeNodesProbeForInsertions:  a 1MJI|1|D|G|54 interacts with 1MJI|1|D|C|30
pMakeNodesProbeForInsertions:  B 1MJI|1|D|C|30 interacts with 1MJI|1|D|G|54
pMakeNodesProbeForInsertions:  B 1MJI|1|D|C|30 interacts with 1MJI|1|D|G|54
pMakeNodes probed for insert:  a=1MJI|1|D|G|54 B=1MJI|1|D|C|30
  3 Basepair    54   30 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1MJI|1|D|C|31
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1MJI|1|D|G|51
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAA'
           RightLetter: 'C'
               Comment: ' // Basepair G51 - C31 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1MJI|1|D|C|31'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1MJI|1|D|G|51'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G54 - C30 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_76709.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.9804
   -4.8803
   -4.8765
   -4.4358

Timestamp 18-Jul-2025 22:48:43
pMakeSCFGModels: Making JAR3D model for motif group IL_76758.2, number 315 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|A|1669 B=5J7L|1|DA|U|1993
  2 Basepair  1669 1993 AU cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|C|1670 B=5J7L|1|DA|U|1991
    Insertion on left  5J7L|1|DA|C|1670
    Insertion on left  5J7L|1|DA|U|1671
    Insertion on left  5J7L|1|DA|A|1672
    Insertion on left  5J7L|1|DA|G|1673
    Insertion on right 5J7L|1|DA|U|1991
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|G|1674 interacts with 5J7L|1|DA|C|1990
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|1990 interacts with 5J7L|1|DA|G|1674
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|1990 interacts with 5J7L|1|DA|G|1674
pMakeNodes probed for insert:  a=5J7L|1|DA|G|1674 B=5J7L|1|DA|C|1990
  3 Basepair  1674 1990 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|1670
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|U|1671
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|1672
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|1673
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5J7L|1|DA|U|1991
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'ACUAG'
           RightLetter: 'UU'
               Comment: ' // Basepair A1669 - U1993 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|1670'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|U|1671'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|1672'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|1673'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5J7L|1|DA|U|1991'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1674 - C1990 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_76758.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.9639
   -4.6646
   -5.4531
   -5.9996
   -6.7524
   -5.3404
   -5.3404

Timestamp 18-Jul-2025 22:48:43
pMakeSCFGModels: Making JAR3D model for motif group IL_77045.1, number 316 of 411
pMakeNodes starting loop:     a=3IGI|1|A|A|149 B=3IGI|1|A|U|225
pMakeNodes making a cluster near strand break a=3IGI|1|A|A|149 B=3IGI|1|A|U|225
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 9 to 11
aa is 5 bb is 9
  2 Cluster   3IGI|1|A|A|149:3IGI|1|A|A|154 3IGI|1|A|A|222:3IGI|1|A|U|225
    LR Inter  3IGI|1|A|A|154 3IGI|1|A|A|222 tHW 
    LR Inter  3IGI|1|A|G|153 3IGI|1|A|A|224 tSW 
    LR Inter  3IGI|1|A|A|149 3IGI|1|A|U|225 cWW 
    LR Inter  3IGI|1|A|A|154 3IGI|1|A|U|225 tSS 
    Left  strand conserved insertion 3IGI|1|A|U|150 at position 2
    Left  strand conserved insertion 3IGI|1|A|A|151 at position 3
pMakeNodesCluster a=6 B=8 at the end
pMakeNodesCluster a=6 B=8 at the end
pMakeNodes probe for inserts:  a=3IGI|1|A|G|155 B=3IGI|1|A|U|221
    Insertion on left  3IGI|1|A|G|155
pMakeNodesProbeForInsertions:  a 3IGI|1|A|G|156 interacts with 3IGI|1|A|U|221
pMakeNodesProbeForInsertions:  B 3IGI|1|A|U|221 interacts with 3IGI|1|A|G|156
pMakeNodesProbeForInsertions:  B 3IGI|1|A|U|221 interacts with 3IGI|1|A|G|156
  3 Initial    155 (1 insertion) and  221 (0 insertion)
pMakeNodes probed for insert:  a=3IGI|1|A|G|156 B=3IGI|1|A|U|221
  4 Basepair   156  221 GU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  9 10 11
pMakeMotifModelFromSSF:   3   Initial Left  6 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|A|154
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 0 0 0 0 1 1 1 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: [9 10 11]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUAGA'
           RightLetter: 'AAU'
               Comment: ' // Cluster node 3IGI|1|A|A|149:3IGI|1|A|A|154 and 3IGI|1|A|A|222:3IGI|1|A|U|225'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.1057
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: []
               Comment: ' // Initial node 3IGI|1|A|G|155 - 3IGI|1|A|U|221 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IGI|1|A|A|154'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G156 - U221 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  9 10 11
pMakeMotifModelFromSSF:   3   Initial Left  6 Right  8
pMakeMotifModelFromSSF:   4     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   7   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_77045.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.9163

Timestamp 18-Jul-2025 22:48:43
pMakeSCFGModels: Making JAR3D model for motif group IL_77278.1, number 317 of 411
pMakeNodes starting loop:     a=8CRE|1|1|C|1183 B=8CRE|1|1|G|1315
  2 Basepair  1183 1315 CG cWW 
No need to probe because of interaction between a=8CRE|1|1|U|1184 B=8CRE|1|1|A|1313
  3 Basepair  1184 1313 UA tWW 
pMakeNodes probe for inserts:  a=8CRE|1|1|C|1185 B=8CRE|1|1|U|1311
    Insertion on left  8CRE|1|1|C|1185
pMakeNodesProbeForInsertions:  a 8CRE|1|1|A|1186 interacts with 8CRE|1|1|U|1311
pMakeNodesProbeForInsertions:  B 8CRE|1|1|U|1311 interacts with 8CRE|1|1|A|1186
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8CRE|1|1|U|1311 interacts with 8CRE|1|1|A|1186
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8CRE|1|1|A|1186 B=8CRE|1|1|U|1311
  4 Basepair  1186 1311 AU tWW 
pMakeNodes probe for inserts:  a=8CRE|1|1|A|1189 B=8CRE|1|1|C|1310
    Insertion on left  8CRE|1|1|A|1189
pMakeNodesProbeForInsertions:  a 8CRE|1|1|G|1190 interacts with 8CRE|1|1|C|1310
pMakeNodesProbeForInsertions:  B 8CRE|1|1|C|1310 interacts with 8CRE|1|1|G|1190
pMakeNodesProbeForInsertions:  B 8CRE|1|1|C|1310 interacts with 8CRE|1|1|G|1190
pMakeNodes probed for insert:  a=8CRE|1|1|G|1190 B=8CRE|1|1|C|1310
  5 Basepair  1190 1310 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|C|1185
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|U|1187
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1183 - G1315 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UC'
           RightLetter: 'A'
               Comment: ' // Basepair U1184 - A1313 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|C|1185'
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'U'
               Comment: ' // Basepair A1186 - U1311 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|U|1187'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1190 - C1310 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  10   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_77278.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.5339
   -7.5339

Timestamp 18-Jul-2025 22:48:44
pMakeSCFGModels: Making JAR3D model for motif group IL_77658.1, number 318 of 411
pMakeNodes starting loop:     a=8ID2|1|C|A|5 B=8ID2|1|C|U|20
  2 Basepair     5   20 AU cWW 
No need to probe because of interaction between a=8ID2|1|C|C|6 B=8ID2|1|C|U|19
  3 Basepair     6   19 CU cWW 
No need to probe because of interaction between a=8ID2|1|C|U|7 B=8ID2|1|C|U|18
  4 Basepair     7   18 UU cWW 
No need to probe because of interaction between a=8ID2|1|C|G|8 B=8ID2|1|C|C|17
  5 Basepair     8   17 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A5 - U20 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'U'
               Comment: ' // Basepair C6 - U19 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U7 - U18 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G8 - C17 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_77658.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0645
   -4.3416
   -4.3416
   -4.7813
   -4.7813
   -7.3237
   -5.1325
   -4.7241
   -4.3416
   -4.7241
   -4.3416
   -6.5027
   -5.1059
   -6.0593
   -6.0629
   -5.8132
   -6.1298
   -6.0629
   -5.8132
   -6.5220
   -4.9965
   -4.9306
   -4.9965
   -6.5220
   -8.1747
   -7.1400
   -7.5081
   -4.3416
   -7.1400
   -7.7223
  -11.9096
   -7.1400
   -4.3416
   -7.1400

Timestamp 18-Jul-2025 22:48:44
pMakeSCFGModels: Making JAR3D model for motif group IL_77691.5, number 319 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|1874 B=5J7L|1|DA|G|1867
  2 Basepair  1874 1867 CG cWW 
No need to probe because of interaction between a=5J7L|1|DA|G|1875 B=5J7L|1|DA|A|1866
  3 Basepair  1875 1866 GA tSH 
No need to probe because of interaction between a=5J7L|1|DA|A|1876 B=5J7L|1|DA|U|1865
  4 Basepair  1876 1865 AU tHS 
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|1877 B=5J7L|1|DA|U|1864
    Insertion on left  5J7L|1|DA|A|1877
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|G|1878 interacts with 5J7L|1|DA|U|1864
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|U|1864 interacts with 5J7L|1|DA|G|1878
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|U|1864 interacts with 5J7L|1|DA|G|1878
pMakeNodes probed for insert:  a=5J7L|1|DA|G|1878 B=5J7L|1|DA|U|1864
  5 Basepair  1878 1864 GU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   6   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|1867
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1874 - G1867 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1875 - A1866 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'U'
               Comment: ' // Basepair A1876 - U1865 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|1867'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1878 - U1864 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   8   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_77691.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7254
   -6.7254
   -7.1963
   -7.4645
   -7.4190
   -7.1963
   -6.9732

Timestamp 18-Jul-2025 22:48:44
pMakeSCFGModels: Making JAR3D model for motif group IL_77870.1, number 320 of 411
pMakeNodes starting loop:     a=4V9F|1|0|C|280 B=4V9F|1|0|G|369
  2 Basepair   280  369 CG cWW 
No need to probe because of interaction between a=4V9F|1|0|U|281 B=4V9F|1|0|C|368
  3 Basepair   281  368 UC bif 
pMakeNodes probe for inserts:  a=4V9F|1|0|C|282 B=4V9F|1|0|G|367
    Insertion on left  4V9F|1|0|C|282
    Insertion on left  4V9F|1|0|U|283
    Insertion on left  4V9F|1|0|C|284
pMakeNodesProbeForInsertions:  a 4V9F|1|0|A|285 interacts with 4V9F|1|0|G|367
pMakeNodesProbeForInsertions:  B 4V9F|1|0|G|367 interacts with 4V9F|1|0|A|285
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4V9F|1|0|G|367 interacts with 4V9F|1|0|A|285
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4V9F|1|0|A|285 B=4V9F|1|0|G|367
  4 Basepair   285  367 AG tHS 
No need to probe because of interaction between a=4V9F|1|0|U|286 B=4V9F|1|0|U|366
  5 Basepair   286  366 UU cWW 
No need to probe because of interaction between a=4V9F|1|0|C|287 B=4V9F|1|0|G|365
  6 Basepair   287  365 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   7   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|C|282
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|U|283
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|C|284
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C280 - G369 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UCUC'
           RightLetter: 'C'
               Comment: ' // Basepair U281 - C368 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|C|282'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|U|283'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|C|284'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A285 - G367 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U286 - U366 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C287 - G365 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  12  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  13   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_77870.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.0100
   -8.2020

Timestamp 18-Jul-2025 22:48:45
pMakeSCFGModels: Making JAR3D model for motif group IL_78349.3, number 321 of 411
pMakeNodes starting loop:     a=4LFB|1|A|U|605 B=4LFB|1|A|G|633
  2 Basepair   605  633 UG cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|G|606 B=4LFB|1|A|G|631
    Insertion on left  4LFB|1|A|G|606
    Insertion on left  4LFB|1|A|A|607
    Insertion on left  4LFB|1|A|A|608
    Insertion on left  4LFB|1|A|A|609
    Insertion on left  4LFB|1|A|G|610
    Insertion on right 4LFB|1|A|G|631
    Insertion on right 4LFB|1|A|G|630
pMakeNodesProbeForInsertions:  a 4LFB|1|A|A|611 interacts with 4LFB|1|A|G|629
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|629 interacts with 4LFB|1|A|A|611
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|629 interacts with 4LFB|1|A|A|611
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4LFB|1|A|A|611 B=4LFB|1|A|G|629
  3 Basepair   611  629 AG cWW 
No need to probe because of interaction between a=4LFB|1|A|C|612 B=4LFB|1|A|G|628
  4 Basepair   612  628 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|606
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|607
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|608
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|A|609
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|610
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|G|631
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|G|630
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGAAAG'
           RightLetter: 'GGG'
               Comment: ' // Basepair U605 - G633 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|G|606'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|607'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                  rpar: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|608'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                  lpar: []
                  rpar: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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      JunctionDeletion: []
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                  lpar: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|A|609'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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                  lpar: []
                  rpar: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|G|610'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|G|631'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|G|630'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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                  rpar: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A611 - G629 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 19
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C612 - G628 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 21
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 12
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 12
pMakeMotifModelFromSSF:  14   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  15     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:  16   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  17  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  18  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  19   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 19
pNextNodeJunction: Found a hairpin at node 19

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_78349.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.1204
  -10.1221

Timestamp 18-Jul-2025 22:48:45
pMakeSCFGModels: Making JAR3D model for motif group IL_78472.1, number 322 of 411
pMakeNodes starting loop:     a=5UNE|1|A|G|31 B=5UNE|1|B|C|14
  2 Basepair    31   14 GC cWW 
pMakeNodes probe for inserts:  a=5UNE|1|A|G|32 B=5UNE|1|B|G|13
    Insertion on left  5UNE|1|A|G|32
    Insertion on right 5UNE|1|B|G|13
pMakeNodesProbeForInsertions:  a 5UNE|1|A|C|33 interacts with 5UNE|1|B|G|12
pMakeNodesProbeForInsertions:  B 5UNE|1|B|G|12 interacts with 5UNE|1|A|C|33
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5UNE|1|B|G|12 interacts with 5UNE|1|A|C|33
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5UNE|1|A|C|33 B=5UNE|1|B|G|12
  3 Basepair    33   12 CG cWW 
No need to probe because of interaction between a=5UNE|1|A|G|34 B=5UNE|1|B|G|11
  4 Basepair    34   11 GG tSH 
pMakeNodes probe for inserts:  a=5UNE|1|A|G|35 B=5UNE|1|B|U|10
    Insertion on left  5UNE|1|A|G|35
    Insertion on left  5UNE|1|A|A|36
    Insertion on left  5UNE|1|A|A|37
pMakeNodesProbeForInsertions:  a 5UNE|1|A|A|38 interacts with 5UNE|1|B|U|10
pMakeNodesProbeForInsertions:  B 5UNE|1|B|U|10 interacts with 5UNE|1|A|A|38
pMakeNodesProbeForInsertions:  B 5UNE|1|B|U|10 interacts with 5UNE|1|A|A|38
pMakeNodes probed for insert:  a=5UNE|1|A|A|38 B=5UNE|1|B|U|10
  5 Basepair    38   10 AU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   6   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5UNE|1|A|G|32
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5UNE|1|B|G|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5UNE|1|A|G|35
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5UNE|1|A|A|36
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5UNE|1|A|A|37
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: 'GC'
               Comment: ' // Basepair G31 - C14 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5UNE|1|A|G|32'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'GGAA'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5UNE|1|B|G|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C33 - G12 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGAA'
           RightLetter: 'G'
               Comment: ' // Basepair G34 - G11 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5UNE|1|A|G|35'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5UNE|1|A|A|36'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5UNE|1|A|A|37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A38 - U10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right 11
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  9
pMakeMotifModelFromSSF:  12   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  14   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  15  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  16   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 16
pNextNodeJunction: Found a hairpin at node 16

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_78472.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.0330

Timestamp 18-Jul-2025 22:48:45
pMakeSCFGModels: Making JAR3D model for motif group IL_78800.1, number 323 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|U|1363 B=8CRE|1|CM|A|1333
pMakeNodes making a cluster near strand break a=8CRE|1|CM|U|1363 B=8CRE|1|CM|A|1333
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 3 and then 6 to 6
aa is 3 bb is 6
  2 Cluster   8CRE|1|CM|U|1363:8CRE|1|CM|C|1365 8CRE|1|CM|A|1333:8CRE|1|CM|A|1333
    LR Inter  8CRE|1|CM|U|1363 8CRE|1|CM|A|1333 cWW 
    LL Inter  8CRE|1|CM|U|1363 8CRE|1|CM|U|1364 cSH 
    LL Inter  8CRE|1|CM|U|1363 8CRE|1|CM|C|1365 cSH 
pMakeNodesCluster a=4 B=5 at the end
pMakeNodesCluster a=4 B=5 at the end
No need to probe because of interaction between a=8CRE|1|CM|U|1366 B=8CRE|1|CM|A|1330
  3 Basepair  1366 1330 UA cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUC'
           RightLetter: 'A'
               Comment: ' // Cluster node 8CRE|1|CM|U|1363:8CRE|1|CM|C|1365 and 8CRE|1|CM|A|1333:8CRE|1|CM|A|1333'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.0630
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1366 - A1330 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  6
pMakeMotifModelFromSSF:   3   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_78800.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.8895
   -4.8895

Timestamp 18-Jul-2025 22:48:45
pMakeSCFGModels: Making JAR3D model for motif group IL_79846.1, number 324 of 411
pMakeNodes starting loop:     a=3Q3Z|1|V|U|60 B=3Q3Z|1|V|A|14
  2 Basepair    60   14 UA cWW 
pMakeNodes probe for inserts:  a=3Q3Z|1|V|A|61 B=3Q3Z|1|V|A|13
pMakeNodesProbeForInsertions:  a 3Q3Z|1|V|A|61 interacts with 3Q3Z|1|V|C|68
pMakeNodesProbeForInsertions:  B 3Q3Z|1|V|A|13 interacts with 3Q3Z|1|V|A|74
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3Q3Z|1|V|A|13 interacts with 3Q3Z|1|V|A|74
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3Q3Z|1|V|A|61 B=3Q3Z|1|V|A|13
pMakeNodes making a cluster near strand break a=3Q3Z|1|V|A|61 B=3Q3Z|1|V|A|13
pMakeNodesCluster: amax is 16 bmin is 17, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 15 and then 18 to 18
aa is 15 bb is 18
  3 Cluster   3Q3Z|1|V|A|61:3Q3Z|1|V|A|74 3Q3Z|1|V|A|13:3Q3Z|1|V|A|13
    LR Inter  3Q3Z|1|V|A|74 3Q3Z|1|V|A|13 cWW 
    LL Inter  3Q3Z|1|V|G|62 3Q3Z|1|V|G|67 tWH 
    LL Inter  3Q3Z|1|V|A|61 3Q3Z|1|V|C|68 bif 
    LL Inter  3Q3Z|1|V|A|70 3Q3Z|1|V|C|71 cSH 
    Left  strand conserved insertion 3Q3Z|1|V|U|63 at position 3
    Left  strand conserved insertion 3Q3Z|1|V|A|64 at position 4
    Left  strand conserved insertion 3Q3Z|1|V|G|65 at position 5
    Left  strand conserved insertion 3Q3Z|1|V|U|66 at position 6
    Left  strand conserved insertion 3Q3Z|1|V|A|69 at position 9
    Left  strand conserved insertion 3Q3Z|1|V|C|72 at position 12
    Left  strand conserved insertion 3Q3Z|1|V|G|73 at position 13
pMakeNodesCluster a=16 B=17 at the end
pMakeNodesCluster a=16 B=17 at the end
No need to probe because of interaction between a=3Q3Z|1|V|C|75 B=3Q3Z|1|V|G|12
  4 Basepair    75   12 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 19
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 19
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8  9 10 11 12 13 14 15 Right 18
pMakeMotifModelFromSSF:   4  Basepair Left 16 Right 17
pMakeMotifModelFromSSF:   5   Hairpin Left 17 Right 16
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 19
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [19×19 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 19
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U60 - A14 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5 6 7 8 9 10 11 12 13 14 15]
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGUAGUGCAACCGA'
           RightLetter: 'A'
               Comment: ' // Cluster node 3Q3Z|1|V|A|61:3Q3Z|1|V|A|74 and 3Q3Z|1|V|A|13:3Q3Z|1|V|A|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×11 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8 9 10 11 12 13 14]
                 Right: 1
      InsertionComment: []
                IBases: [11×2 double]
    InteractionComment: {1×11 cell}
      JunctionDeletion: []
          InterIndices: [11×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [3 4 5 6 9 12 13]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 16
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 16
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C75 - G12 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 17
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 17
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 19
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 19
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8  9 10 11 12 13 14 15 Right 18
pMakeMotifModelFromSSF:   4   Initial Left 16 Right 17
pMakeMotifModelFromSSF:   5  Basepair Left 16 Right 17
pMakeMotifModelFromSSF:   6   Hairpin Left 17 Right 16
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_79846.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.4084

Timestamp 18-Jul-2025 22:48:45
pMakeSCFGModels: Making JAR3D model for motif group IL_79895.1, number 325 of 411
pMakeNodes starting loop:     a=8CRE|1|1|G|2742 B=8CRE|1|1|C|2760
  2 Basepair  2742 2760 GC cWW 
pMakeNodes probe for inserts:  a=8CRE|1|1|U|2743 B=8CRE|1|1|G|2759
    Insertion on left  8CRE|1|1|U|2743
    Insertion on left  8CRE|1|1|C|2744
pMakeNodesProbeForInsertions:  a 8CRE|1|1|C|2745 interacts with 8CRE|1|1|G|2759
pMakeNodesProbeForInsertions:  B 8CRE|1|1|G|2759 interacts with 8CRE|1|1|C|2745
pMakeNodesProbeForInsertions:  B 8CRE|1|1|G|2759 interacts with 8CRE|1|1|C|2745
pMakeNodes probed for insert:  a=8CRE|1|1|C|2745 B=8CRE|1|1|G|2759
  3 Basepair  2745 2759 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|U|2743
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|C|2744
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUC'
           RightLetter: 'C'
               Comment: ' // Basepair G2742 - C2760 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|U|2743'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|C|2744'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C2745 - G2759 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_79895.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.0280
   -5.0284

Timestamp 18-Jul-2025 22:48:45
pMakeSCFGModels: Making JAR3D model for motif group IL_80209.1, number 326 of 411
pMakeNodes starting loop:     a=4LCK|1|F|U|37 B=4LCK|1|F|A|71
  2 Basepair    37   71 UA cWW 
No need to probe because of interaction between a=4LCK|1|F|G|38 B=4LCK|1|F|G|70
  3 Basepair    38   70 GG cHW 
pMakeNodes probe for inserts:  a=4LCK|1|F|A|39 B=4LCK|1|F|G|69
    Insertion on left  4LCK|1|F|A|39
    Insertion on left  4LCK|1|F|U|40
    Insertion on left  4LCK|1|F|U|41
    Insertion on left  4LCK|1|F|A|42
    Insertion on left  4LCK|1|F|G|43
    Insertion on left  4LCK|1|F|C|44
    Insertion on left  4LCK|1|F|G|45
pMakeNodesProbeForInsertions:  a 4LCK|1|F|C|47 interacts with 4LCK|1|F|G|69
pMakeNodesProbeForInsertions:  B 4LCK|1|F|G|69 interacts with 4LCK|1|F|C|47
pMakeNodesProbeForInsertions:  B 4LCK|1|F|G|69 interacts with 4LCK|1|F|C|47
pMakeNodes probed for insert:  a=4LCK|1|F|C|47 B=4LCK|1|F|G|69
  4 Basepair    47   69 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   5   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LCK|1|F|A|39
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LCK|1|F|U|40
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LCK|1|F|U|41
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LCK|1|F|A|42
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LCK|1|F|G|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LCK|1|F|C|44
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LCK|1|F|G|45
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U37 - A71 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAUUAGCG'
           RightLetter: 'G'
               Comment: ' // Basepair G38 - G70 cHW '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LCK|1|F|A|39'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LCK|1|F|U|40'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LCK|1|F|U|41'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LCK|1|F|A|42'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LCK|1|F|G|43'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LCK|1|F|C|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LCK|1|F|G|45'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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                  lpar: []
                  rpar: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
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                  lpar: []
                  rpar: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C47 - G69 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 21
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 12
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 11
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  16     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  17   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  18  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  19   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 19
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 1 of 1, pair 2,12 for nucleotide 2 (G) making self BPh with edge 1
pNextNodeJunction: Found a hairpin at node 19

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_80209.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.0533

Timestamp 18-Jul-2025 22:48:46
pMakeSCFGModels: Making JAR3D model for motif group IL_80231.1, number 327 of 411
pMakeNodes starting loop:     a=5XTM|1|B|G|8 B=5XTM|1|B|C|39
  2 Basepair     8   39 GC cWW 
No need to probe because of interaction between a=5XTM|1|B|A|9 B=5XTM|1|B|C|38
  3 Basepair     9   38 AC tSH 
No need to probe because of interaction between a=5XTM|1|B|U|10 B=5XTM|1|B|A|37
  4 Basepair    10   37 UA tSH 
No need to probe because of interaction between a=5XTM|1|B|G|11 B=5XTM|1|B|A|36
  5 Basepair    11   36 GA tSH 
pMakeNodes probe for inserts:  a=5XTM|1|B|A|12 B=5XTM|1|B|U|35
    Insertion on left  5XTM|1|B|A|12
pMakeNodesProbeForInsertions:  a 5XTM|1|B|A|14 interacts with 5XTM|1|B|U|35
pMakeNodesProbeForInsertions:  B 5XTM|1|B|U|35 interacts with 5XTM|1|B|A|14
pMakeNodesProbeForInsertions:  B 5XTM|1|B|U|35 interacts with 5XTM|1|B|A|14
pMakeNodes probed for insert:  a=5XTM|1|B|A|14 B=5XTM|1|B|U|35
  6 Basepair    14   35 AU cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5XTM|1|B|A|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G8 - C39 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A9 - C38 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U10 - A37 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'A'
               Comment: ' // Basepair G11 - A36 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5XTM|1|B|A|12'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A14 - U35 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_80231.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.2618
   -9.1226

Timestamp 18-Jul-2025 22:48:46
pMakeSCFGModels: Making JAR3D model for motif group IL_80298.1, number 328 of 411
pMakeNodes starting loop:     a=4WT8|1|DV|C|25 B=4WT8|1|DV|G|10
  2 Basepair    25   10 CG cWW 
pMakeNodes probe for inserts:  a=4WT8|1|DV|A|26 B=4WT8|1|DV|A|7
    Insertion on left  4WT8|1|DV|A|26
    Insertion on left  4WT8|1|DV|G|27
    Insertion on left  4WT8|1|DV|G|28
    Insertion on left  4WT8|1|DV|G|29
    Insertion on left  4WT8|1|DV|G|30
    Insertion on left  4WT8|1|DV|A|31
    Insertion on left  4WT8|1|DV|U|32
    Insertion on left  4WT8|1|DV|U|33
    Insertion on left  4WT8|1|DV|G|34
    Insertion on left  4WT8|1|DV|A|35
    Insertion on left  4WT8|1|DV|A|36
    Insertion on left  4WT8|1|DV|A|37
    Insertion on left  4WT8|1|DV|A|38
    Insertion on left  4WT8|1|DV|U|39
    Insertion on left  4WT8|1|DV|U|40
    Insertion on left  4WT8|1|DV|C|41
    Insertion on left  4WT8|1|DV|C|42
    Insertion on left  4WT8|1|DV|G|43
    Insertion on left  4WT8|1|DV|A|44
    Insertion on left  4WT8|1|DV|G|45
pMakeNodesProbeForInsertions:  a 4WT8|1|DV|U|46 interacts with 4WT8|1|DV|A|7
pMakeNodesProbeForInsertions:  B 4WT8|1|DV|A|7 interacts with 4WT8|1|DV|U|46
pMakeNodesProbeForInsertions:  B 4WT8|1|DV|A|7 interacts with 4WT8|1|DV|U|46
pMakeNodes probed for insert:  a=4WT8|1|DV|U|46 B=4WT8|1|DV|A|7
  3 Basepair    46    7 UA cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 24
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 24
pMakeMotifModelFromSSF:   3  Basepair Left 22 Right 23
pMakeMotifModelFromSSF:   4   Hairpin Left 23 Right 22
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|U|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|A|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|G|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|C|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|A|26
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|G|27
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|G|28
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|G|29
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|G|30
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|A|31
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|U|32
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|U|33
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|G|34
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|A|35
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|A|36
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|A|37
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|A|38
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|U|39
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|U|40
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WT8|1|DV|C|41
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 24
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [24×24 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 24
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-21 8.1893e-20 8.1893e-19 8.1893e-18 8.1893e-17 8.1893e-16 8.1893e-15 8.1893e-14 8.1893e-13 8.1893e-12 … ]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAGGGGAUUGAAAAUUCCGAG'
           RightLetter: 'G'
               Comment: ' // Basepair C25 - G10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WT8|1|DV|U|8'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 23
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
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               Comment: ' // Fixed node on left for 4WT8|1|DV|A|9'
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Node 6

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 7

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 8

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 9

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Node 10

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Node 11

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Node 12

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Node 13

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Node 14

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 15

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Node 16

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Node 17

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Node 18

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Node 19

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Node 20

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Node 21

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Node 22

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Node 23

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Node 24

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Node 25

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Node 26

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Node 27

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Node 28

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Node 29

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Node 30

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        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 31

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 32
             LeftIndex: 16
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WT8|1|DV|A|36'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 32

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 33
             LeftIndex: 17
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 33

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 34
             LeftIndex: 17
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WT8|1|DV|A|37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 34

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 35
             LeftIndex: 18
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 35

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 36
             LeftIndex: 18
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WT8|1|DV|A|38'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 36

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 37
             LeftIndex: 19
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 37

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 38
             LeftIndex: 19
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WT8|1|DV|U|39'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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                  lpar: []
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Node 38

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 39
             LeftIndex: 20
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 39

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 40
             LeftIndex: 20
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WT8|1|DV|U|40'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 40

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 41
             LeftIndex: 21
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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                  lpar: []
                  rpar: []
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Node 41

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 42
             LeftIndex: 21
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WT8|1|DV|C|41'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 42

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 43
             LeftIndex: 22
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 43

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 44
             LeftIndex: 22
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U46 - A7 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 44

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 46
             LeftIndex: 23
            RightIndex: 22
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 23
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 24
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 24
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 23
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 23
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 23
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 23
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 23
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 23
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 23
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 23
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 23
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 23
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 23
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 23
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 23
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 23
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 23
pMakeMotifModelFromSSF:  18   Initial Left 10 Right 23
pMakeMotifModelFromSSF:  19     Fixed Left 10 Right 23
pMakeMotifModelFromSSF:  20   Initial Left 11 Right 23
pMakeMotifModelFromSSF:  21     Fixed Left 11 Right 23
pMakeMotifModelFromSSF:  22   Initial Left 12 Right 23
pMakeMotifModelFromSSF:  23     Fixed Left 12 Right 23
pMakeMotifModelFromSSF:  24   Initial Left 13 Right 23
pMakeMotifModelFromSSF:  25     Fixed Left 13 Right 23
pMakeMotifModelFromSSF:  26   Initial Left 14 Right 23
pMakeMotifModelFromSSF:  27     Fixed Left 14 Right 23
pMakeMotifModelFromSSF:  28   Initial Left 15 Right 23
pMakeMotifModelFromSSF:  29     Fixed Left 15 Right 23
pMakeMotifModelFromSSF:  30   Initial Left 16 Right 23
pMakeMotifModelFromSSF:  31     Fixed Left 16 Right 23
pMakeMotifModelFromSSF:  32   Initial Left 17 Right 23
pMakeMotifModelFromSSF:  33     Fixed Left 17 Right 23
pMakeMotifModelFromSSF:  34   Initial Left 18 Right 23
pMakeMotifModelFromSSF:  35     Fixed Left 18 Right 23
pMakeMotifModelFromSSF:  36   Initial Left 19 Right 23
pMakeMotifModelFromSSF:  37     Fixed Left 19 Right 23
pMakeMotifModelFromSSF:  38   Initial Left 20 Right 23
pMakeMotifModelFromSSF:  39     Fixed Left 20 Right 23
pMakeMotifModelFromSSF:  40   Initial Left 21 Right 23
pMakeMotifModelFromSSF:  41     Fixed Left 21 Right 23
pMakeMotifModelFromSSF:  42   Initial Left 22 Right 23
pMakeMotifModelFromSSF:  43  Basepair Left 22 Right 23
pMakeMotifModelFromSSF:  44   Hairpin Left 23 Right 22
pNextNodeJunction: Found a hairpin at node 44
pNextNodeJunction: Found a hairpin at node 44

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_80298.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -17.8619

Timestamp 18-Jul-2025 22:48:46
pMakeSCFGModels: Making JAR3D model for motif group IL_80398.1, number 329 of 411
pMakeNodes starting loop:     a=4TS2|1|X|G|14 B=4TS2|1|Y|C|85
  2 Basepair    14   85 GC cWW 
pMakeNodes probe for inserts:  a=4TS2|1|X|A|15 B=4TS2|1|Y|A|84
    Insertion on left  4TS2|1|X|A|15
    Insertion on left  4TS2|1|X|A|16
pMakeNodesProbeForInsertions:  a 4TS2|1|X|A|17 interacts with 4TS2|1|Y|A|84
pMakeNodesProbeForInsertions:  B 4TS2|1|Y|A|84 interacts with 4TS2|1|X|A|17
pMakeNodesProbeForInsertions:  B 4TS2|1|Y|A|84 interacts with 4TS2|1|X|A|17
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4TS2|1|X|A|17 B=4TS2|1|Y|A|84
pMakeNodes making a cluster near strand break a=4TS2|1|X|A|17 B=4TS2|1|Y|A|84
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 4 and then 5 to 7
aa is 4 bb is 5
  3 Cluster   4TS2|1|X|A|17:4TS2|1|X|A|17 4TS2|1|Y|U|82:4TS2|1|Y|A|84
    LR Inter  4TS2|1|X|A|17 4TS2|1|Y|U|82 cWW 
    LR Inter  4TS2|1|X|A|17 4TS2|1|Y|A|84 cSW 
    Right strand conserved insertion 4TS2|1|Y|A|83 at position 2
pMakeNodesCluster a=5 B=4 at the end
pMakeNodesCluster a=5 B=4 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3   Cluster Left  4 Right  5  6  7
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4TS2|1|X|A|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4TS2|1|X|A|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAA'
           RightLetter: 'C'
               Comment: ' // Basepair G14 - C85 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4TS2|1|X|A|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: 2
              NormCons: 0.2504

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4TS2|1|X|A|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: 4
            RightIndex: [5 6 7]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: 'UAA'
               Comment: ' // Cluster node 4TS2|1|X|A|17:4TS2|1|X|A|17 and 4TS2|1|Y|U|82:4TS2|1|Y|A|84'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: 2
              NormCons: 0.2504

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7   Cluster Left  4 Right  5  6  7
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  4
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 9
pUpdateModelWithSSF: IL_80398.1 allow insertions from initial node 8?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_80398.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.2704

Timestamp 18-Jul-2025 22:48:46
pMakeSCFGModels: Making JAR3D model for motif group IL_80412.1, number 330 of 411
pMakeNodes starting loop:     a=6P2H|1|A|A|45 B=6P2H|1|A|U|25
  2 Basepair    45   25 AU cWW 
No need to probe because of interaction between a=6P2H|1|A|G|46 B=6P2H|1|A|A|23
  3 Basepair    46   23 GA tSW 
pMakeNodes probe for inserts:  a=6P2H|1|A|C|47 B=6P2H|1|A|U|22
    Insertion on left  6P2H|1|A|C|47
    Insertion on left  6P2H|1|A|C|48
    Insertion on left  6P2H|1|A|U|49
    Insertion on left  6P2H|1|A|C|50
    Insertion on left  6P2H|1|A|C|51
pMakeNodesProbeForInsertions:  a 6P2H|1|A|A|52 interacts with 6P2H|1|A|U|22
pMakeNodesProbeForInsertions:  B 6P2H|1|A|U|22 interacts with 6P2H|1|A|A|52
pMakeNodesProbeForInsertions:  B 6P2H|1|A|U|22 interacts with 6P2H|1|A|A|52
pMakeNodes probed for insert:  a=6P2H|1|A|A|52 B=6P2H|1|A|U|22
  4 Basepair    52   22 AU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6P2H|1|A|A|24
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6P2H|1|A|U|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6P2H|1|A|A|45
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6P2H|1|A|G|46
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6P2H|1|A|C|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A45 - U25 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GCCUCC'
           RightLetter: 'A'
               Comment: ' // Basepair G46 - A23 tSW '
              NumLoops: []
                  Edge: 6
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6P2H|1|A|A|24'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6P2H|1|A|U|25'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6P2H|1|A|A|45'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6P2H|1|A|G|46'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6P2H|1|A|C|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A52 - U22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right  9
pMakeMotifModelFromSSF:  11   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  13   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  15   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a hairpin at node 15

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_80412.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.1335

Timestamp 18-Jul-2025 22:48:46
pMakeSCFGModels: Making JAR3D model for motif group IL_80604.6, number 331 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|G|143 B=8P9A|1|sR|C|172
  2 Basepair   143  172 GC cWW 
No need to probe because of interaction between a=8P9A|1|sR|U|144 B=8P9A|1|sR|A|171
  3 Basepair   144  171 UA cWW 
No need to probe because of interaction between a=8P9A|1|sR|A|145 B=8P9A|1|sR|A|169
  4 Basepair   145  169 AA tWH 
No need to probe because of interaction between a=8P9A|1|sR|U|146 B=8P9A|1|sR|A|168
  5 Basepair   146  168 UA tWH 
No need to probe because of interaction between a=8P9A|1|sR|A|147 B=8P9A|1|sR|U|167
  6 Basepair   147  167 AU tHW 
No need to probe because of interaction between a=8P9A|1|sR|A|148 B=8P9A|1|sR|C|166
  7 Basepair   148  166 AC tHW 
No need to probe because of interaction between a=8P9A|1|sR|C|149 B=8P9A|1|sR|G|165
  8 Basepair   149  165 CG cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 11
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G143 - C172 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U144 - A171 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A145 - A169 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U146 - A168 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A147 - U167 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A148 - C166 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C149 - G165 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 11
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   9   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_80604.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2485
   -7.1671
   -7.1671

Timestamp 18-Jul-2025 22:48:47
pMakeSCFGModels: Making JAR3D model for motif group IL_80926.1, number 332 of 411
pMakeNodes starting loop:     a=3BBM|1|B|G|6 B=3BBM|1|A|C|9
  2 Basepair     6    9 GC cWW 
No need to probe because of interaction between a=3BBM|1|B|A|7 B=3BBM|1|A|C|8
  3 Basepair     7    8 AC cWW 
No need to probe because of interaction between a=3BBM|1|B|G|8 B=3BBM|1|A|U|7
  4 Basepair     8    7 GU tSH 
No need to probe because of interaction between a=3BBM|1|B|A|9 B=3BBM|1|A|A2M|5
  5 Basepair     9    5 AA tHS 
pMakeNodes probe for inserts:  a=3BBM|1|B|A|10 B=3BBM|1|A|C|4
    Insertion on left  3BBM|1|B|A|10
pMakeNodesProbeForInsertions:  a 3BBM|1|B|G|11 interacts with 3BBM|1|A|C|4
pMakeNodesProbeForInsertions:  B 3BBM|1|A|C|4 interacts with 3BBM|1|B|G|11
pMakeNodesProbeForInsertions:  B 3BBM|1|A|C|4 interacts with 3BBM|1|B|G|11
pMakeNodes probed for insert:  a=3BBM|1|B|G|11 B=3BBM|1|A|C|4
  6 Basepair    11    4 GC cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3BBM|1|A|C|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G6 - C9 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A7 - C8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G8 - U7 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'A'
               Comment: ' // Basepair A9 - A5 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3BBM|1|A|C|8'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G11 - C4 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   6     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   7   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_80926.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3453
   -6.3453
   -6.3453
   -6.3453
   -6.8266
   -6.3453
   -6.3453

Timestamp 18-Jul-2025 22:48:47
pMakeSCFGModels: Making JAR3D model for motif group IL_81392.1, number 333 of 411
pMakeNodes starting loop:     a=6LT7|1|C|C|52 B=6LT7|1|C|G|37
  2 Basepair    52   37 CG cWW 
pMakeNodes probe for inserts:  a=6LT7|1|C|C|53 B=6LT7|1|C|A|34
    Insertion on left  6LT7|1|C|C|53
    Insertion on left  6LT7|1|C|C|54
    Insertion on left  6LT7|1|C|C|55
    Insertion on left  6LT7|1|C|U|56
    Insertion on left  6LT7|1|C|U|57
    Insertion on left  6LT7|1|C|U|58
    Insertion on left  6LT7|1|C|C|59
    Insertion on right 6LT7|1|C|A|34
    Insertion on right 6LT7|1|C|A|32
pMakeNodesProbeForInsertions:  a 6LT7|1|C|G|61 interacts with 6LT7|1|C|C|28
pMakeNodesProbeForInsertions:  B 6LT7|1|C|C|28 interacts with 6LT7|1|C|G|61
pMakeNodesProbeForInsertions:  B 6LT7|1|C|C|28 interacts with 6LT7|1|C|G|61
pMakeNodes probed for insert:  a=6LT7|1|C|G|61 B=6LT7|1|C|C|28
  3 Basepair    61   28 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   4   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6LT7|1|C|U|29
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6LT7|1|C|A|30
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6LT7|1|C|C|31
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6LT7|1|C|A|32
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6LT7|1|C|C|33
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6LT7|1|C|A|34
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6LT7|1|C|C|35
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6LT7|1|C|C|53
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6LT7|1|C|C|52
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
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        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
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           RightLetter: ''
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                  Edge: [13×13 double]
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              SubsProb: []
                     Z: []
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Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CCCCUUUC'
           RightLetter: 'AAG'
               Comment: ' // Basepair C52 - G37 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
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Node 3

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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             LeftIndex: 2
            RightIndex: 12
             Insertion: []
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        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6LT7|1|C|U|29'
              NumLoops: []
                  Edge: 1
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                Delete: 1.0000e-03
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                     Z: 1
           MiddleIndex: []
                     P: []
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Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: ''
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Node 5

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 6

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           RightLetter: []
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Node 7

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 8

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           RightLetter: []
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Node 9

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 10

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       rightLengthDist: [0.9999 1.0000e-04]
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           RightLetter: []
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Node 11

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 12

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Node 13

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Node 14

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Node 15

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Node 16

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Node 17

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Node 18

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Node 19

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Node 20

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                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 22
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G61 - C28 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 24
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 12
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 12
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 12
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 12
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 12
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  19     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  20   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  21  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  22   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 22
pNextNodeJunction: Found a hairpin at node 22

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_81392.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -16.2142

Timestamp 18-Jul-2025 22:48:47
pMakeSCFGModels: Making JAR3D model for motif group IL_81516.2, number 334 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|G|496 B=5J7L|1|DA|C|484
  2 Basepair   496  484 GC cWW 
No need to probe because of interaction between a=5J7L|1|DA|A|497 B=5J7L|1|DA|A|483
pMakeNodes making a cluster near strand break a=5J7L|1|DA|A|497 B=5J7L|1|DA|A|483
pMakeNodesCluster: amax is 12 bmin is 13, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 12 and then 13 to 15
aa is 12 bb is 13
  3 Cluster   5J7L|1|DA|A|497:5J7L|1|DA|C|509 5J7L|1|DA|G|481:5J7L|1|DA|A|483
    LR Inter  5J7L|1|DA|G|506 5J7L|1|DA|G|481 tSS 
    LR Inter  5J7L|1|DA|C|509 5J7L|1|DA|G|481 cWW 
    LR Inter  5J7L|1|DA|A|497 5J7L|1|DA|A|482 cWS 
    LR Inter  5J7L|1|DA|A|507 5J7L|1|DA|A|482 tHH 
    LR Inter  5J7L|1|DA|A|497 5J7L|1|DA|A|483 tSH 
    LL Inter  5J7L|1|DA|U|499 5J7L|1|DA|A|503 tWH 
    LL Inter  5J7L|1|DA|G|500 5J7L|1|DA|A|505 tSH 
    LL Inter  5J7L|1|DA|G|498 5J7L|1|DA|G|506 bif 
    Left  strand conserved insertion 5J7L|1|DA|A|501 at position 5
    Left  strand conserved insertion 5J7L|1|DA|A|502 at position 6
pMakeNodesCluster a=13 B=12 at the end
pMakeNodesCluster a=13 B=12 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8  9 10 11 12 Right 13 14 15
pMakeMotifModelFromSSF:   4   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G496 - C484 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5 6 7 8 9 10 11 12]
            RightIndex: [13 14 15]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGUGAAAAGAC'
           RightLetter: 'GAA'
               Comment: ' // Cluster node 5J7L|1|DA|A|497:5J7L|1|DA|C|509 and 5J7L|1|DA|G|481:5J7L|1|DA|A|483'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×10 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8 9 10 11]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [10×2 double]
    InteractionComment: {1×10 cell}
      JunctionDeletion: []
          InterIndices: [10×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [5 6]
         RightNotInter: [1×0 double]
              NormCons: 0.0040

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8  9 10 11 12 Right 13 14 15
pMakeMotifModelFromSSF:   4   Initial Left 13 Right 12
pMakeMotifModelFromSSF:   5   Hairpin Left 13 Right 12
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_81516.2 allow insertions from initial node 4?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_81516.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.0432
   -6.8905
   -7.6790
   -6.7486
   -7.7971
   -7.7971

Timestamp 18-Jul-2025 22:48:48
pMakeSCFGModels: Making JAR3D model for motif group IL_81522.2, number 335 of 411
pMakeNodes starting loop:     a=4M6D|1|H|G|28 B=4M6D|1|H|C|39
pMakeNodes making a cluster near strand break a=4M6D|1|H|G|28 B=4M6D|1|H|C|39
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 3 and then 6 to 6
aa is 3 bb is 6
  2 Cluster   4M6D|1|H|G|28:4M6D|1|H|A|31 4M6D|1|H|C|39:4M6D|1|H|C|39
    LR Inter  4M6D|1|H|G|28 4M6D|1|H|C|39 cWW 
    LR Inter  4M6D|1|H|A|31 4M6D|1|H|C|39 cWS 
    Left  strand conserved insertion 4M6D|1|H|U|30 at position 2
pMakeNodesCluster a=4 B=5 at the end
pMakeNodesCluster a=4 B=5 at the end
No need to probe because of interaction between a=4M6D|1|H|C|32 B=4M6D|1|H|G|36
  3 Basepair    32   36 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 0 0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUA'
           RightLetter: 'C'
               Comment: ' // Cluster node 4M6D|1|H|G|28:4M6D|1|H|A|31 and 4M6D|1|H|C|39:4M6D|1|H|C|39'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2498
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C32 - G36 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  6
pMakeMotifModelFromSSF:   3   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_81522.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3660
   -6.3660
   -9.5309

Timestamp 18-Jul-2025 22:48:48
pMakeSCFGModels: Making JAR3D model for motif group IL_81731.1, number 336 of 411
pMakeNodes starting loop:     a=4M6D|1|H|G|12 B=4M6D|1|H|C|48
  2 Basepair    12   48 GC cWW 
No need to probe because of interaction between a=4M6D|1|H|G|13 B=4M6D|1|H|A|47
  3 Basepair    13   47 GA cWW 
No need to probe because of interaction between a=4M6D|1|H|C|14 B=4M6D|1|H|G|46
  4 Basepair    14   46 CG cWW 
No need to probe because of interaction between a=4M6D|1|H|U|15 B=4M6D|1|H|A|45
  5 Basepair    15   45 UA cWW 
pMakeNodes probe for inserts:  a=4M6D|1|H|A|16 B=4M6D|1|H|C|44
    Insertion on left  4M6D|1|H|A|16
    Insertion on left  4M6D|1|H|A|17
pMakeNodesProbeForInsertions:  a 4M6D|1|H|A|18 interacts with 4M6D|1|H|U|22
pMakeNodesProbeForInsertions:  B 4M6D|1|H|C|44 interacts with 4M6D|1|H|G|23
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4M6D|1|H|C|44 interacts with 4M6D|1|H|G|23
pMakeNodes probed for insert:  a=4M6D|1|H|A|18 B=4M6D|1|H|C|44
pMakeNodes making a cluster near strand break a=4M6D|1|H|A|18 B=4M6D|1|H|C|44
pMakeNodesCluster: amax is 12 bmin is 13, use_amax is 1
pMakeNodesCluster: Cluster goes from 7 to 12 and then 13 to 13
aa is 12 bb is 13
  6 Cluster   4M6D|1|H|A|18:4M6D|1|H|G|23 4M6D|1|H|C|44:4M6D|1|H|C|44
    LR Inter  4M6D|1|H|G|23 4M6D|1|H|C|44 cWW 
    LL Inter  4M6D|1|H|A|18 4M6D|1|H|U|22 tWW 
    Left  strand conserved insertion 4M6D|1|H|G|19 at position 2
    Left  strand conserved insertion 4M6D|1|H|A|20 at position 3
    Left  strand conserved insertion 4M6D|1|H|G|21 at position 4
pMakeNodesCluster a=13 B=12 at the end
pMakeNodesCluster a=13 B=12 at the end
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 15
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 14
pMakeMotifModelFromSSF:   6   Cluster Left  7  8  9 10 11 12 Right 13
pMakeMotifModelFromSSF:   7   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4M6D|1|H|A|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4M6D|1|H|A|17
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [17×17 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G12 - C48 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G13 - A47 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C14 - G46 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UAA'
           RightLetter: 'A'
               Comment: ' // Basepair U15 - A45 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4M6D|1|H|A|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4M6D|1|H|A|17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 11
             LeftIndex: [7 8 9 10 11 12]
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGAGUG'
           RightLetter: 'C'
               Comment: ' // Cluster node 4M6D|1|H|A|18:4M6D|1|H|G|23 and 4M6D|1|H|C|44:4M6D|1|H|C|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 1

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 15
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 14
pMakeMotifModelFromSSF:   6     Fixed Left  5 Right 13
pMakeMotifModelFromSSF:   7   Initial Left  6 Right 13
pMakeMotifModelFromSSF:   8     Fixed Left  6 Right 13
pMakeMotifModelFromSSF:   9   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  10   Cluster Left  7  8  9 10 11 12 Right 13
pMakeMotifModelFromSSF:  11   Initial Left 13 Right 12
pMakeMotifModelFromSSF:  12   Hairpin Left 13 Right 12
pNextNodeJunction: Found a hairpin at node 12
pUpdateModelWithSSF: IL_81731.1 allow insertions from initial node 11?
ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9899    0.0100    0.0001


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_81731.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.6226

Timestamp 18-Jul-2025 22:48:48
pMakeSCFGModels: Making JAR3D model for motif group IL_81831.1, number 337 of 411
pMakeNodes starting loop:     a=4R4V|1|A|U|719 B=4R4V|1|A|A|756
  2 Basepair   719  756 UA cWW 
pMakeNodes probe for inserts:  a=4R4V|1|A|A|720 B=4R4V|1|A|C|755
    Insertion on left  4R4V|1|A|A|720
pMakeNodesProbeForInsertions:  a 4R4V|1|A|G|722 interacts with 4R4V|1|A|C|755
pMakeNodesProbeForInsertions:  B 4R4V|1|A|C|755 interacts with 4R4V|1|A|G|722
pMakeNodesProbeForInsertions:  B 4R4V|1|A|C|755 interacts with 4R4V|1|A|G|722
pMakeNodes probed for insert:  a=4R4V|1|A|G|722 B=4R4V|1|A|C|755
  3 Basepair   722  755 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4R4V|1|A|A|720
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: 'A'
               Comment: ' // Basepair U719 - A756 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4R4V|1|A|A|720'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G722 - C755 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_81831.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.5044
   -4.8112

Timestamp 18-Jul-2025 22:48:48
pMakeSCFGModels: Making JAR3D model for motif group IL_82107.4, number 338 of 411
pMakeNodes starting loop:     a=5WTK|1|B|A|3 B=5WTK|1|B|U|23
  2 Basepair     3   23 AU cWW 
No need to probe because of interaction between a=5WTK|1|B|C|4 B=5WTK|1|B|G|20
  3 Basepair     4   20 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  2
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A3 - U23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C4 - G20 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 3
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  2
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_82107.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.2514
   -6.2514
   -5.7199
   -5.7199
   -5.9582
   -6.2514
   -5.8879
   -4.4918
   -4.4918
   -6.5678
   -4.4918
   -6.5678
   -4.6241
   -4.6241
   -7.4359
   -7.2903
   -7.4359
   -4.6952
   -4.4918
   -5.9251
   -7.1179
   -5.8879
   -4.4918
   -4.7851
   -5.9233
   -4.6457
  -12.1520
   -6.5678
   -8.9144
   -8.9144

Timestamp 18-Jul-2025 22:48:48
pMakeSCFGModels: Making JAR3D model for motif group IL_82292.1, number 339 of 411
pMakeNodes starting loop:     a=8SSW|1|C|C|11 B=8SSW|1|D|G|16
  2 Basepair    11   16 CG cWW 
pMakeNodes probe for inserts:  a=8SSW|1|C|G|12 B=8SSW|1|D|A|15
    Insertion on left  8SSW|1|C|G|12
    Insertion on right 8SSW|1|D|A|15
pMakeNodesProbeForInsertions:  a 8SSW|1|C|C|13 interacts with 8SSW|1|D|A|14
pMakeNodesProbeForInsertions:  B 8SSW|1|D|A|14 interacts with 8SSW|1|C|C|13
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8SSW|1|D|A|14 interacts with 8SSW|1|C|C|13
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8SSW|1|C|C|13 B=8SSW|1|D|A|14
  3 Basepair    13   14 CA cWW 
No need to probe because of interaction between a=8SSW|1|C|A|14 B=8SSW|1|D|C|13
  4 Basepair    14   13 AC cWW 
pMakeNodes probe for inserts:  a=8SSW|1|C|A|15 B=8SSW|1|D|G|12
    Insertion on left  8SSW|1|C|A|15
    Insertion on right 8SSW|1|D|G|12
pMakeNodesProbeForInsertions:  a 8SSW|1|C|G|16 interacts with 8SSW|1|D|C|11
pMakeNodesProbeForInsertions:  B 8SSW|1|D|C|11 interacts with 8SSW|1|C|G|16
pMakeNodesProbeForInsertions:  B 8SSW|1|D|C|11 interacts with 8SSW|1|C|G|16
pMakeNodes probed for insert:  a=8SSW|1|C|G|16 B=8SSW|1|D|C|11
  5 Basepair    16   11 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8SSW|1|C|G|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8SSW|1|D|A|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8SSW|1|C|A|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8SSW|1|D|G|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CG'
           RightLetter: 'AG'
               Comment: ' // Basepair C11 - G16 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8SSW|1|C|G|12'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'AA'
           RightLetter: 'GC'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8SSW|1|D|A|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C13 - A14 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'GC'
               Comment: ' // Basepair A14 - C13 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8SSW|1|C|A|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8SSW|1|D|G|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G16 - C11 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_82292.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.8989
  -10.2013
  -12.4874

Timestamp 18-Jul-2025 22:48:49
pMakeSCFGModels: Making JAR3D model for motif group IL_82426.6, number 340 of 411
pMakeNodes starting loop:     a=8K85|1|B|A|40 B=8K85|1|A|U|14
  2 Basepair    40   14 AU cWW 
pMakeNodes probe for inserts:  a=8K85|1|B|G|41 B=8K85|1|A|G|13
    Insertion on right 8K85|1|A|G|13
pMakeNodesProbeForInsertions:  a 8K85|1|B|G|41 interacts with 8K85|1|B|G|46
pMakeNodesProbeForInsertions:  B 8K85|1|A|G|12 interacts with 8K85|1|B|G|46
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8K85|1|A|G|12 interacts with 8K85|1|B|G|46
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8K85|1|B|G|41 B=8K85|1|A|G|12
pMakeNodes making a cluster near strand break a=8K85|1|B|G|41 B=8K85|1|A|G|12
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 8 and then 11 to 12
aa is 8 bb is 11
  3 Cluster   8K85|1|B|G|41:8K85|1|B|U|49 8K85|1|A|G|11:8K85|1|A|G|12
    LR Inter  8K85|1|B|G|48 8K85|1|A|G|11 cHW 
    LR Inter  8K85|1|B|G|46 8K85|1|A|G|12 cHW 
    LL Inter  8K85|1|B|G|41 8K85|1|B|G|46 cHW 
    LL Inter  8K85|1|B|G|44 8K85|1|B|G|48 cHW 
    LL Inter  8K85|1|B|U|42 8K85|1|B|U|49 tSW 
    Left  strand conserved insertion 8K85|1|B|U|45 at position 4
pMakeNodesCluster a=9 B=10 at the end
pMakeNodesCluster a=9 B=10 at the end
No need to probe because of interaction between a=8K85|1|B|G|50 B=8K85|1|A|C|10
  4 Basepair    50   10 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6  7  8 Right 11 12
pMakeMotifModelFromSSF:   4  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   5   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8K85|1|B|U|47
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'GU'
               Comment: ' // Basepair A40 - U14 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8K85|1|B|U|47'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7]
                 Right: [1 2]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 4
         RightNotInter: [1×0 double]
              NormCons: 0.2070

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [2 3 4 5 6 7 8]
            RightIndex: [11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUGUGGU'
           RightLetter: 'GG'
               Comment: ' // Cluster node 8K85|1|B|G|41:8K85|1|B|U|49 and 8K85|1|A|G|11:8K85|1|A|G|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7]
                 Right: [1 2]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 4
         RightNotInter: [1×0 double]
              NormCons: 0.2070

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G50 - C10 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 13
pMakeMotifModelFromSSF:   4   Initial Left  2 Right 12
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6  7  8 Right 11 12
pMakeMotifModelFromSSF:   6   Initial Left  9 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   8   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_82426.6_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3293
   -5.7415
   -6.3293
   -5.7415
   -5.7415
   -5.7415

Timestamp 18-Jul-2025 22:48:49
pMakeSCFGModels: Making JAR3D model for motif group IL_82683.2, number 341 of 411
pMakeNodes starting loop:     a=7QQX|1|A|C|40 B=7QQX|1|A|G|29
  2 Basepair    40   29 CG cWW 
pMakeNodes probe for inserts:  a=7QQX|1|A|A|41 B=7QQX|1|A|G|27
    Insertion on left  7QQX|1|A|A|41
    Insertion on left  7QQX|1|A|A|42
    Insertion on left  7QQX|1|A|G|43
    Insertion on right 7QQX|1|A|G|27
pMakeNodesProbeForInsertions:  a 7QQX|1|A|U|45 interacts with 7QQX|1|A|A|26
pMakeNodesProbeForInsertions:  B 7QQX|1|A|A|26 interacts with 7QQX|1|A|U|45
pMakeNodesProbeForInsertions:  B 7QQX|1|A|A|26 interacts with 7QQX|1|A|U|45
pMakeNodes probed for insert:  a=7QQX|1|A|U|45 B=7QQX|1|A|A|26
  3 Basepair    45   26 UA cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QQX|1|A|G|27
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QQX|1|A|A|28
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QQX|1|A|G|29
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7QQX|1|A|A|42
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAAG'
           RightLetter: 'GG'
               Comment: ' // Basepair C40 - G29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QQX|1|A|G|27'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QQX|1|A|A|28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QQX|1|A|G|29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7QQX|1|A|A|42'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U45 - A26 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  10   Initial Left  5 Right  6
pMakeMotifModelFromSSF:  11  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  12   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_82683.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.2651
   -3.2651
   -3.2651
   -3.2651
   -3.2651
   -3.2651
   -3.2651
   -3.2651
   -3.2651
   -3.2651
   -3.2651

Timestamp 18-Jul-2025 22:48:49
pMakeSCFGModels: Making JAR3D model for motif group IL_82706.1, number 342 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|U|1095 B=8P9A|1|sR|A|1036
  2 Basepair  1095 1036 UA cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|U|1097 B=8P9A|1|sR|G|1035
    Insertion on left  8P9A|1|sR|U|1097
    Insertion on left  8P9A|1|sR|U|1099
    Insertion on right 8P9A|1|sR|G|1035
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|G|1101 interacts with 8P9A|1|sR|C|1034
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|C|1034 interacts with 8P9A|1|sR|G|1101
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|C|1034 interacts with 8P9A|1|sR|G|1101
pMakeNodes probed for insert:  a=8P9A|1|sR|G|1101 B=8P9A|1|sR|C|1034
  3 Basepair  1101 1034 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|G|1035
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|A|1036
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|U|1097
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UUU'
           RightLetter: 'GA'
               Comment: ' // Basepair U1095 - A1036 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|G|1035'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|A|1036'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|U|1097'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1101 - C1034 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_82706.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.9736
   -5.9736

Timestamp 18-Jul-2025 22:48:49
pMakeSCFGModels: Making JAR3D model for motif group IL_82741.2, number 343 of 411
pMakeNodes starting loop:     a=8CRE|1|1|C|3190 B=8CRE|1|1|G|3225
  2 Basepair  3190 3225 CG cWW 
pMakeNodes probe for inserts:  a=8CRE|1|1|A|3191 B=8CRE|1|1|U|3223
    Insertion on left  8CRE|1|1|A|3191
    Insertion on left  8CRE|1|1|A|3192
    Insertion on left  8CRE|1|1|C|3193
pMakeNodesProbeForInsertions:  a 8CRE|1|1|G|3194 interacts with 8CRE|1|1|U|3223
pMakeNodesProbeForInsertions:  B 8CRE|1|1|U|3223 interacts with 8CRE|1|1|G|3194
pMakeNodesProbeForInsertions:  B 8CRE|1|1|U|3223 interacts with 8CRE|1|1|G|3194
pMakeNodes probed for insert:  a=8CRE|1|1|G|3194 B=8CRE|1|1|U|3223
  3 Basepair  3194 3223 GU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|A|3191
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|A|3192
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|C|3193
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAAC'
           RightLetter: 'G'
               Comment: ' // Basepair C3190 - G3225 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|A|3191'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|A|3192'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|C|3193'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G3194 - U3223 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:  10   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_82741.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.8801
   -5.8801
   -8.4785

Timestamp 18-Jul-2025 22:48:49
pMakeSCFGModels: Making JAR3D model for motif group IL_82968.1, number 344 of 411
pMakeNodes starting loop:     a=7JRT|1|A|C|11 B=7JRT|1|A|G|57
  2 Basepair    11   57 CG cWW 
pMakeNodes probe for inserts:  a=7JRT|1|A|G|12 B=7JRT|1|A|G|56
    Insertion on left  7JRT|1|A|G|12
    Insertion on left  7JRT|1|A|G|13
    Insertion on left  7JRT|1|A|A|14
    Insertion on left  7JRT|1|A|G|15
    Insertion on left  7JRT|1|A|G|16
    Insertion on left  7JRT|1|A|C|17
    Insertion on left  7JRT|1|A|A|18
pMakeNodesProbeForInsertions:  a 7JRT|1|A|C|19 interacts with 7JRT|1|A|G|56
pMakeNodesProbeForInsertions:  B 7JRT|1|A|G|56 interacts with 7JRT|1|A|C|19
pMakeNodesProbeForInsertions:  B 7JRT|1|A|G|56 interacts with 7JRT|1|A|C|19
pMakeNodes probed for insert:  a=7JRT|1|A|C|19 B=7JRT|1|A|G|56
  3 Basepair    19   56 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   4   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|G|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|G|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|A|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|G|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|G|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|C|17
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|A|18
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGGAGGCA'
           RightLetter: 'G'
               Comment: ' // Basepair C11 - G57 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|G|12'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|G|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|A|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|G|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|G|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|C|17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|A|18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C19 - G56 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 10
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  17  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  18   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a hairpin at node 18

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_82968.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3500
   -6.3500

Timestamp 18-Jul-2025 22:48:49
pMakeSCFGModels: Making JAR3D model for motif group IL_83149.1, number 345 of 411
pMakeNodes starting loop:     a=8CRE|1|1|U|1295 B=8CRE|1|1|A|1201
  2 Basepair  1295 1201 UA cWW 
No need to probe because of interaction between a=8CRE|1|1|G|1296 B=8CRE|1|1|A|1200
  3 Basepair  1296 1200 GA tSH 
No need to probe because of interaction between a=8CRE|1|1|A|1297 B=8CRE|1|1|A|1199
  4 Basepair  1297 1199 AA tHH 
pMakeNodes probe for inserts:  a=8CRE|1|1|A|1299 B=8CRE|1|1|A|1198
    Insertion on left  8CRE|1|1|A|1299
    Insertion on left  8CRE|1|1|A|1300
    Insertion on left  8CRE|1|1|G|1303
    Insertion on left  8CRE|1|1|A|1304
    Insertion on left  8CRE|1|1|U|1305
    Insertion on left  8CRE|1|1|G|1306
    Insertion on left  8CRE|1|1|G|1307
    Insertion on left  8CRE|1|1|C|1308
    Insertion on right 8CRE|1|1|A|1198
    Insertion on right 8CRE|1|1|C|1197
    Insertion on right 8CRE|1|1|A|1196
    Insertion on right 8CRE|1|1|C|1195
    Insertion on right 8CRE|1|1|C|1194
    Insertion on right 8CRE|1|1|A|1193
pMakeNodesProbeForInsertions:  a 8CRE|1|1|G|1309 interacts with 8CRE|1|1|A|1191
pMakeNodesProbeForInsertions:  B 8CRE|1|1|A|1191 interacts with 8CRE|1|1|G|1309
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8CRE|1|1|A|1191 interacts with 8CRE|1|1|G|1309
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8CRE|1|1|G|1309 B=8CRE|1|1|A|1191
  5 Basepair  1309 1191 GA cWW 
No need to probe because of interaction between a=8CRE|1|1|C|1310 B=8CRE|1|1|G|1190
  6 Basepair  1310 1190 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 24
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 24
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 23
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 22
pMakeMotifModelFromSSF:   5  Basepair Left 12 Right 15
pMakeMotifModelFromSSF:   6  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:   7   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|A|1193
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|C|1194
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|C|1195
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|A|1196
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|C|1197
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|A|1198
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|A|1199
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|A|1200
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|1|G|1303
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|1|G|1302
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|1|U|1301
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|1|A|1300
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|1|A|1299
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|1|A|1298
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 24
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [24×24 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 24
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1295 - A1201 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 23
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1296 - A1200 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 22
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAAGAUGGC'
           RightLetter: 'ACCACAA'
               Comment: ' // Basepair A1297 - A1199 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|A|1193'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|C|1194'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 14
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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      JunctionDeletion: []
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                  lpar: []
                  rpar: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|C|1195'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                IBases: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|A|1196'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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                  rpar: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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                 Right: []
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                  lpar: []
                  rpar: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|C|1197'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|A|1198'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 10
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 10
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|A|1199'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 11
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
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            RightIndex: 21
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        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|A|1200'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 12
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 22
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        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|1|G|1303'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 12
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 24
             LeftIndex: 12
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             Insertion: []
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        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|1|G|1302'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
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Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 12
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             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 26
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        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|1|U|1301'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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Node 26

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 27
             LeftIndex: 12
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             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 27

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 28
             LeftIndex: 12
            RightIndex: 18
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|1|A|1300'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 28

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 29
             LeftIndex: 12
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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Node 29

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 30
             LeftIndex: 12
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|1|A|1299'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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      InsertionComment: []
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Node 30

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 31
             LeftIndex: 12
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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Node 31

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 32
             LeftIndex: 12
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|1|A|1298'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                  lpar: []
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Node 32

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 33
             LeftIndex: 12
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
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Node 33

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 34
             LeftIndex: 12
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1309 - A1191 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 34

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 35
             LeftIndex: 13
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1310 - G1190 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 35

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 37
             LeftIndex: 14
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 14
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 24
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 24
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 23
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 22
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right 21
pMakeMotifModelFromSSF:   6   Initial Left  5 Right 21
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right 21
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 21
pMakeMotifModelFromSSF:   9     Fixed Left  6 Right 21
pMakeMotifModelFromSSF:  10   Initial Left  7 Right 21
pMakeMotifModelFromSSF:  11     Fixed Left  7 Right 21
pMakeMotifModelFromSSF:  12   Initial Left  8 Right 21
pMakeMotifModelFromSSF:  13     Fixed Left  8 Right 21
pMakeMotifModelFromSSF:  14   Initial Left  9 Right 21
pMakeMotifModelFromSSF:  15     Fixed Left  9 Right 21
pMakeMotifModelFromSSF:  16   Initial Left 10 Right 21
pMakeMotifModelFromSSF:  17     Fixed Left 10 Right 21
pMakeMotifModelFromSSF:  18   Initial Left 11 Right 21
pMakeMotifModelFromSSF:  19     Fixed Left 11 Right 21
pMakeMotifModelFromSSF:  20   Initial Left 12 Right 21
pMakeMotifModelFromSSF:  21     Fixed Left 12 Right 21
pMakeMotifModelFromSSF:  22   Initial Left 12 Right 20
pMakeMotifModelFromSSF:  23     Fixed Left 12 Right 20
pMakeMotifModelFromSSF:  24   Initial Left 12 Right 19
pMakeMotifModelFromSSF:  25     Fixed Left 12 Right 19
pMakeMotifModelFromSSF:  26   Initial Left 12 Right 18
pMakeMotifModelFromSSF:  27     Fixed Left 12 Right 18
pMakeMotifModelFromSSF:  28   Initial Left 12 Right 17
pMakeMotifModelFromSSF:  29     Fixed Left 12 Right 17
pMakeMotifModelFromSSF:  30   Initial Left 12 Right 16
pMakeMotifModelFromSSF:  31     Fixed Left 12 Right 16
pMakeMotifModelFromSSF:  32   Initial Left 12 Right 15
pMakeMotifModelFromSSF:  33  Basepair Left 12 Right 15
pMakeMotifModelFromSSF:  34  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:  35   Hairpin Left 14 Right 13
pNextNodeJunction: Found a hairpin at node 35
pNextNodeJunction: Found a hairpin at node 35

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_83149.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -14.6354
  -14.6354

Timestamp 18-Jul-2025 22:48:50
pMakeSCFGModels: Making JAR3D model for motif group IL_83150.2, number 346 of 411
pMakeNodes starting loop:     a=4WF9|1|X|G|1356 B=4WF9|1|X|C|1370
pMakeNodes making a cluster near strand break a=4WF9|1|X|G|1356 B=4WF9|1|X|C|1370
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 6 to 7
aa is 5 bb is 6
  2 Cluster   4WF9|1|X|G|1356:4WF9|1|X|G|1360 4WF9|1|X|C|1368:4WF9|1|X|C|1370
    LR Inter  4WF9|1|X|G|1357 4WF9|1|X|C|1368 tHH 
    LR Inter  4WF9|1|X|G|1360 4WF9|1|X|C|1368 cWW 
    LR Inter  4WF9|1|X|G|1356 4WF9|1|X|C|1370 cWW 
    LR Inter  4WF9|1|X|A|1359 4WF9|1|X|C|1370 cWS 
    Left  strand conserved insertion 4WF9|1|X|A|1358 at position 3
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  3 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  6  7
pMakeMotifModelFromSSF:   3   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: [6 7]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGAAG'
           RightLetter: 'CC'
               Comment: ' // Cluster node 4WF9|1|X|G|1356:4WF9|1|X|G|1360 and 4WF9|1|X|C|1368:4WF9|1|X|C|1370'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2]
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
          LeftNotInter: 3
         RightNotInter: [1×0 double]
              NormCons: 0.0622

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right  6  7
pMakeMotifModelFromSSF:   3   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 4
pUpdateModelWithSSF: IL_83150.2 allow insertions from initial node 3?
ans =

    0.9960    0.0040    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9960    0.0040    0.0000


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_83150.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.8464
   -5.8464
   -6.1547
   -6.1547

Timestamp 18-Jul-2025 22:48:50
pMakeSCFGModels: Making JAR3D model for motif group IL_83389.2, number 347 of 411
pMakeNodes starting loop:     a=4V9F|1|0|A|2095 B=4V9F|1|0|U|2650
  2 Basepair  2095 2650 AU cWW 
No need to probe because of interaction between a=4V9F|1|0|G|2097 B=4V9F|1|0|C|2647
  3 Basepair  2097 2647 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  2
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A2095 - U2650 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G2097 - C2647 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 3
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  2
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_83389.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7185
   -6.0550
   -6.0550
   -6.1545
   -6.1545

Timestamp 18-Jul-2025 22:48:50
pMakeSCFGModels: Making JAR3D model for motif group IL_84251.1, number 348 of 411
pMakeNodes starting loop:     a=7EDT|1|A|U|5 B=7EDT|1|B|G|20
  2 Basepair     5   20 UG cWW 
No need to probe because of interaction between a=7EDT|1|A|C|6 B=7EDT|1|B|C|19
  3 Basepair     6   19 CC tWH 
No need to probe because of interaction between a=7EDT|1|A|C|7 B=7EDT|1|B|C|18
  4 Basepair     7   18 CC tHS 
No need to probe because of interaction between a=7EDT|1|A|G|8 B=7EDT|1|B|U|17
  5 Basepair     8   17 GU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U5 - G20 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C6 - C19 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C7 - C18 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G8 - U17 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_84251.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.9051
   -9.4912

Timestamp 18-Jul-2025 22:48:50
pMakeSCFGModels: Making JAR3D model for motif group IL_84409.1, number 349 of 411
pMakeNodes starting loop:     a=1NBS|1|B|C|184 B=1NBS|1|B|G|226
pMakeNodes making a cluster near strand break a=1NBS|1|B|C|184 B=1NBS|1|B|G|226
pMakeNodesCluster: amax is 13 bmin is 14, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 12 and then 15 to 23
aa is 12 bb is 15
  2 Cluster   1NBS|1|B|C|184:1NBS|1|B|G|196 1NBS|1|B|G|217:1NBS|1|B|G|226
    LR Inter  1NBS|1|B|G|190 1NBS|1|B|G|217 cHW 
    LR Inter  1NBS|1|B|A|187 1NBS|1|B|U|218 cSS 
    LR Inter  1NBS|1|B|A|185 1NBS|1|B|G|220 tHH 
    LR Inter  1NBS|1|B|C|184 1NBS|1|B|A|221 tSS 
    LR Inter  1NBS|1|B|G|188 1NBS|1|B|A|222 tSW 
    LR Inter  1NBS|1|B|G|193 1NBS|1|B|C|223 cHW 
    LR Inter  1NBS|1|B|C|192 1NBS|1|B|G|224 cWH 
    LR Inter  1NBS|1|B|C|184 1NBS|1|B|G|226 cWW 
    LL Inter  1NBS|1|B|A|187 1NBS|1|B|A|191 tWH 
    LL Inter  1NBS|1|B|A|191 1NBS|1|B|C|192 cSH 
    LL Inter  1NBS|1|B|G|190 1NBS|1|B|A|195 cSS 
    LL Inter  1NBS|1|B|U|189 1NBS|1|B|G|196 cWS 
    RR Inter  1NBS|1|B|U|218 1NBS|1|B|A|222 tWH 
    RR Inter  1NBS|1|B|A|222 1NBS|1|B|C|223 cSH 
    Left  strand conserved insertion 1NBS|1|B|C|186 at position 3
    Right strand conserved insertion 1NBS|1|B|G|219 at position 3
pMakeNodesCluster a=13 B=14 at the end
pMakeNodesCluster a=13 B=14 at the end
No need to probe because of interaction between a=1NBS|1|B|U|197 B=1NBS|1|B|A|216
  3 Basepair   197  216 UA cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 23
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6  7  8  9 10 11 12 Right 15 16 17 18 19 20 21 22 23
pMakeMotifModelFromSSF:   3  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:   4   Hairpin Left 14 Right 13
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 23
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [23×23 double]
         Extensibility: [0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5 6 7 8 9 10 11 12]
            RightIndex: [15 16 17 18 19 20 21 22 23]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CACAGUGACGAG'
           RightLetter: 'GUGGAACGG'
               Comment: ' // Cluster node 1NBS|1|B|C|184:1NBS|1|B|G|196 and 1NBS|1|B|G|217:1NBS|1|B|G|226'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×16 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6 7 8 9 10 11 12]
                 Right: [1 2 3 4 5 6 7 8 9]
      InsertionComment: []
                IBases: [16×2 double]
    InteractionComment: {1×16 cell}
      JunctionDeletion: []
          InterIndices: [16×2 double]
          LeftNotInter: 3
         RightNotInter: 3
              NormCons: 7.6045e-06
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 13
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 13
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U197 - A216 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 14
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 14
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 23
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6  7  8  9 10 11 12 Right 15 16 17 18 19 20 21 22 23
pMakeMotifModelFromSSF:   3   Initial Left 13 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left 13 Right 14
pMakeMotifModelFromSSF:   5   Hairpin Left 14 Right 13
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_84409.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -14.6431

Timestamp 18-Jul-2025 22:48:52
pMakeSCFGModels: Making JAR3D model for motif group IL_84476.1, number 350 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|C|3349 B=8P9A|1|AR|G|3356
  2 Basepair  3349 3356 CG cWW 
No need to probe because of interaction between a=8P9A|1|AR|C|3350 B=8P9A|1|AR|G|3353
  3 Basepair  3350 3353 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  2
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [4×4 double]
         Extensibility: [0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C3349 - G3356 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C3350 - G3353 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 2
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 3
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  4
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  4
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  3
pMakeMotifModelFromSSF:   4   Hairpin Left  3 Right  2
pNextNodeJunction: Found a hairpin at node 4
pNextNodeJunction: Found a hairpin at node 4

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_84476.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.2784
   -4.2784
   -5.7068
   -4.2784
   -5.7068
   -4.2784
   -7.7194
   -8.7864
   -8.7864
   -7.5379
   -5.9691
   -4.5440
   -9.1073

Timestamp 18-Jul-2025 22:48:53
pMakeSCFGModels: Making JAR3D model for motif group IL_84665.1, number 351 of 411
pMakeNodes starting loop:     a=7QR4|1|B|C|6 B=7QR4|1|B|G|31
  2 Basepair     6   31 CG cWW 
pMakeNodes probe for inserts:  a=7QR4|1|B|C|7 B=7QR4|1|B|A|30
    Insertion on left  7QR4|1|B|C|7
pMakeNodesProbeForInsertions:  a 7QR4|1|B|A|8 interacts with 7QR4|1|B|A|30
pMakeNodesProbeForInsertions:  B 7QR4|1|B|A|30 interacts with 7QR4|1|B|A|8
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 7QR4|1|B|A|30 interacts with 7QR4|1|B|A|8
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=7QR4|1|B|A|8 B=7QR4|1|B|A|30
  3 Basepair     8   30 AA cSW 
pMakeNodes probe for inserts:  a=7QR4|1|B|C|9 B=7QR4|1|B|C|29
    Insertion on left  7QR4|1|B|C|9
    Insertion on left  7QR4|1|B|A|10
    Insertion on left  7QR4|1|B|G|11
    Insertion on left  7QR4|1|B|C|12
    Insertion on left  7QR4|1|B|A|13
    Insertion on left  7QR4|1|B|G|14
    Insertion on left  7QR4|1|B|A|15
    Insertion on left  7QR4|1|B|A|16
pMakeNodesProbeForInsertions:  a 7QR4|1|B|G|17 interacts with 7QR4|1|B|C|29
pMakeNodesProbeForInsertions:  B 7QR4|1|B|C|29 interacts with 7QR4|1|B|G|17
pMakeNodesProbeForInsertions:  B 7QR4|1|B|C|29 interacts with 7QR4|1|B|G|17
pMakeNodes probed for insert:  a=7QR4|1|B|G|17 B=7QR4|1|B|C|29
  4 Basepair    17   29 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:   5   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR4|1|B|C|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR4|1|B|C|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR4|1|B|A|10
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR4|1|B|G|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR4|1|B|C|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR4|1|B|A|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR4|1|B|G|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR4|1|B|A|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7QR4|1|B|A|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CC'
           RightLetter: 'G'
               Comment: ' // Basepair C6 - G31 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR4|1|B|C|7'
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'ACAGCAGAA'
           RightLetter: 'A'
               Comment: ' // Basepair A8 - A30 cSW '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR4|1|B|C|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR4|1|B|A|10'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR4|1|B|G|11'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR4|1|B|C|12'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR4|1|B|A|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 9
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR4|1|B|G|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR4|1|B|A|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 20
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 21
             LeftIndex: 11
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7QR4|1|B|A|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 22
             LeftIndex: 12
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 23
             LeftIndex: 12
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G17 - C29 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 26
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 14
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right 14
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 13
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 13
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 13
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 13
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 13
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 13
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 13
pMakeMotifModelFromSSF:  15   Initial Left  9 Right 13
pMakeMotifModelFromSSF:  16     Fixed Left  9 Right 13
pMakeMotifModelFromSSF:  17   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  18     Fixed Left 10 Right 13
pMakeMotifModelFromSSF:  19   Initial Left 11 Right 13
pMakeMotifModelFromSSF:  20     Fixed Left 11 Right 13
pMakeMotifModelFromSSF:  21   Initial Left 12 Right 13
pMakeMotifModelFromSSF:  22  Basepair Left 12 Right 13
pMakeMotifModelFromSSF:  23   Hairpin Left 13 Right 12
pNextNodeJunction: Found a hairpin at node 23
pNextNodeJunction: Found a hairpin at node 23

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_84665.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.8969

Timestamp 18-Jul-2025 22:48:53
pMakeSCFGModels: Making JAR3D model for motif group IL_84694.2, number 352 of 411
pMakeNodes starting loop:     a=8CRE|1|1|C|30 B=8CRE|1|1|G|52
  2 Basepair    30   52 CG cWW 
pMakeNodes probe for inserts:  a=8CRE|1|1|U|31 B=8CRE|1|1|A|51
    Insertion on left  8CRE|1|1|U|31
    Insertion on right 8CRE|1|1|A|51
pMakeNodesProbeForInsertions:  a 8CRE|1|1|G|32 interacts with 8CRE|1|1|A|50
pMakeNodesProbeForInsertions:  B 8CRE|1|1|A|50 interacts with 8CRE|1|1|G|32
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8CRE|1|1|A|50 interacts with 8CRE|1|1|G|32
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8CRE|1|1|G|32 B=8CRE|1|1|A|50
  3 Basepair    32   50 GA tSH 
No need to probe because of interaction between a=8CRE|1|1|A|33 B=8CRE|1|1|U|49
  4 Basepair    33   49 AU tHW 
No need to probe because of interaction between a=8CRE|1|1|A|34 B=8CRE|1|1|A|47
  5 Basepair    34   47 AA tHH 
No need to probe because of interaction between a=8CRE|1|1|C|35 B=8CRE|1|1|C|46
  6 Basepair    35   46 CC tHS 
No need to probe because of interaction between a=8CRE|1|1|U|36 B=8CRE|1|1|U|45
  7 Basepair    36   45 UU cWW 
No need to probe because of interaction between a=8CRE|1|1|U|37 B=8CRE|1|1|A|44
  8 Basepair    37   44 UA cWW 
  9 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right 13
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right 12
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   7  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   8  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   9   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|U|31
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|1|A|50
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CU'
           RightLetter: 'AG'
               Comment: ' // Basepair C30 - G52 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|U|31'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|1|A|50'
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G32 - A50 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A33 - U49 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A34 - A47 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C35 - C46 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U36 - U45 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U37 - A44 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 15
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 15
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 15
pMakeMotifModelFromSSF:   6   Initial Left  3 Right 14
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right 14
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right 13
pMakeMotifModelFromSSF:   9  Basepair Left  5 Right 12
pMakeMotifModelFromSSF:  10  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:  11  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:  12  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  13   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_84694.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.8383
   -9.8383
  -11.5994

Timestamp 18-Jul-2025 22:48:53
pMakeSCFGModels: Making JAR3D model for motif group IL_85033.2, number 353 of 411
pMakeNodes starting loop:     a=1D4R|1|A|G|4 B=1D4R|1|B|C|25
  2 Basepair     4   25 GC cWW 
No need to probe because of interaction between a=1D4R|1|A|A|5 B=1D4R|1|B|C|24
  3 Basepair     5   24 AC cWW 
No need to probe because of interaction between a=1D4R|1|A|C|6 B=1D4R|1|B|A|23
  4 Basepair     6   23 CA cWW 
No need to probe because of interaction between a=1D4R|1|A|C|7 B=1D4R|1|B|G|22
  5 Basepair     7   22 CG cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G4 - C25 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A5 - C24 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C6 - A23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C7 - G22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_85033.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.2002
   -7.2002
   -8.3304
   -8.3304
   -7.2002
   -7.2002
  -10.3826
   -7.2002
   -9.3405
   -8.3526
   -8.3047
   -6.9488
   -6.9488
   -9.5355
   -9.8386
   -6.3446
   -7.0991
  -10.6667
   -6.8018
   -6.3446
   -8.7100
   -8.9998
   -6.3446
   -8.7100
   -8.9998
   -8.4302
   -9.1750
   -8.4302
  -10.8104
  -11.3539
  -11.3539
  -11.3539
  -10.1924
  -10.1924
  -11.3539

Timestamp 18-Jul-2025 22:48:53
pMakeSCFGModels: Making JAR3D model for motif group IL_85222.1, number 354 of 411
pMakeNodes starting loop:     a=4LFB|1|A|G|1143 B=4LFB|1|A|C|1128
  2 Basepair  1143 1128 GC cWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|G|1144 B=4LFB|1|A|G|1127
    Insertion on left  4LFB|1|A|G|1144
    Insertion on left  4LFB|1|A|C|1145
    Insertion on left  4LFB|1|A|A|1146
    Insertion on left  4LFB|1|A|C|1147
    Insertion on left  4LFB|1|A|U|1148
    Insertion on right 4LFB|1|A|G|1127
    Insertion on right 4LFB|1|A|U|1126
pMakeNodesProbeForInsertions:  a 4LFB|1|A|C|1149 interacts with 4LFB|1|A|G|1124
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|1124 interacts with 4LFB|1|A|C|1149
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|1124 interacts with 4LFB|1|A|C|1149
pMakeNodes probed for insert:  a=4LFB|1|A|C|1149 B=4LFB|1|A|G|1124
  3 Basepair  1149 1124 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|U|1125
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|U|1126
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|1127
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|C|1128
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|G|1143
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|C|1147
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|A|1146
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGCACU'
           RightLetter: 'UGC'
               Comment: ' // Basepair G1143 - C1128 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|U|1125'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|U|1126'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|G|1127'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|C|1128'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|G|1143'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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                  lpar: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|C|1147'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|A|1146'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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                 Right: []
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                  lpar: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1149 - G1124 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 20
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  14   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  15     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  16   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  17  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  18   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a hairpin at node 18

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_85222.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.7794

Timestamp 18-Jul-2025 22:48:54
pMakeSCFGModels: Making JAR3D model for motif group IL_85498.1, number 355 of 411
pMakeNodes starting loop:     a=8VVJ|1|A|U|11 B=8VVJ|1|A|G|35
  2 Basepair    11   35 UG cWW 
pMakeNodes probe for inserts:  a=8VVJ|1|A|G|12 B=8VVJ|1|A|G|34
    Insertion on left  8VVJ|1|A|G|12
    Insertion on left  8VVJ|1|A|G|13
    Insertion on left  8VVJ|1|A|C|14
    Insertion on left  8VVJ|1|A|G|15
    Insertion on left  8VVJ|1|A|A|17
    Insertion on left  8VVJ|1|A|C|18
    Insertion on left  8VVJ|1|A|A|19
    Insertion on right 8VVJ|1|A|G|34
pMakeNodesProbeForInsertions:  a 8VVJ|1|A|G|20 interacts with 8VVJ|1|A|C|33
pMakeNodesProbeForInsertions:  B 8VVJ|1|A|C|33 interacts with 8VVJ|1|A|G|20
pMakeNodesProbeForInsertions:  B 8VVJ|1|A|C|33 interacts with 8VVJ|1|A|G|20
pMakeNodes probed for insert:  a=8VVJ|1|A|G|20 B=8VVJ|1|A|C|33
  3 Basepair    20   33 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   4   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8VVJ|1|A|G|12
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8VVJ|1|A|G|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8VVJ|1|A|C|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8VVJ|1|A|G|15
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8VVJ|1|A|A|16
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8VVJ|1|A|A|17
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8VVJ|1|A|C|18
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8VVJ|1|A|C|33
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGGCGACA'
           RightLetter: 'GG'
               Comment: ' // Basepair U11 - G35 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8VVJ|1|A|G|12'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
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Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8VVJ|1|A|G|13'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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                  rpar: []
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Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                  lpar: []
                  rpar: []
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Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8VVJ|1|A|C|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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               subtype: []
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Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8VVJ|1|A|G|15'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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               subtype: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8VVJ|1|A|A|16'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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               subtype: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8VVJ|1|A|A|17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8VVJ|1|A|C|18'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8VVJ|1|A|C|33'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G20 - C33 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 22
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 11
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  18   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  19  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  20   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Found a hairpin at node 20

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_85498.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.5936

Timestamp 18-Jul-2025 22:48:54
pMakeSCFGModels: Making JAR3D model for motif group IL_85536.2, number 356 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|G|1527 B=8CRE|1|CM|C|1558
  2 Basepair  1527 1558 GC cWW 
No need to probe because of interaction between a=8CRE|1|CM|G|1528 B=8CRE|1|CM|A|1557
  3 Basepair  1528 1557 GA tSH 
No need to probe because of interaction between a=8CRE|1|CM|G|1529 B=8CRE|1|CM|A|1556
  4 Basepair  1529 1556 GA tSH 
No need to probe because of interaction between a=8CRE|1|CM|A|1530 B=8CRE|1|CM|C|1555
  5 Basepair  1530 1555 AC tHS 
No need to probe because of interaction between a=8CRE|1|CM|U|1531 B=8CRE|1|CM|U|1554
  6 Basepair  1531 1554 UU cWW 
No need to probe because of interaction between a=8CRE|1|CM|A|1532 B=8CRE|1|CM|U|1553
  7 Basepair  1532 1553 AU cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1527 - C1558 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1528 - A1557 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G1529 - A1556 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A1530 - C1555 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U1531 - U1554 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A1532 - U1553 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_85536.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.2052
   -9.2052
   -8.9304
   -8.9304
   -9.0418
   -9.0418
  -11.2640
  -20.6055

Timestamp 18-Jul-2025 22:48:54
pMakeSCFGModels: Making JAR3D model for motif group IL_85599.2, number 357 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|U|2081 B=5J7L|1|DA|G|2239
  2 Basepair  2081 2239 UG cWW 
No need to probe because of interaction between a=5J7L|1|DA|A|2082 B=5J7L|1|DA|G|2237
  3 Basepair  2082 2237 AG tHS 
No need to probe because of interaction between a=5J7L|1|DA|G|2083 B=5J7L|1|DA|U|2236
  4 Basepair  2083 2236 GU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U2081 - G2239 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A2082 - G2237 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G2083 - U2236 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_85599.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.8583
   -4.8583
   -4.9976
   -4.8583
   -4.9976
   -5.6752
   -5.8145
   -5.8145
   -7.0993

Timestamp 18-Jul-2025 22:48:54
pMakeSCFGModels: Making JAR3D model for motif group IL_85630.1, number 358 of 411
pMakeNodes starting loop:     a=4LVW|1|A|U|77 B=4LVW|1|A|G|9
  2 Basepair    77    9 UG cWW 
No need to probe because of interaction between a=4LVW|1|A|G|78 B=4LVW|1|A|A|8
  3 Basepair    78    8 GA tSH 
pMakeNodes probe for inserts:  a=4LVW|1|A|C|79 B=4LVW|1|A|U|7
    Insertion on left  4LVW|1|A|C|79
    Insertion on left  4LVW|1|A|A|80
    Insertion on left  4LVW|1|A|U|81
    Insertion on left  4LVW|1|A|C|82
    Insertion on left  4LVW|1|A|C|83
    Insertion on right 4LVW|1|A|U|7
    Insertion on right 4LVW|1|A|G|6
pMakeNodesProbeForInsertions:  a 4LVW|1|A|G|84 interacts with 4LVW|1|A|A|5
pMakeNodesProbeForInsertions:  B 4LVW|1|A|A|5 interacts with 4LVW|1|A|G|84
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4LVW|1|A|A|5 interacts with 4LVW|1|A|G|84
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4LVW|1|A|G|84 B=4LVW|1|A|A|5
  4 Basepair    84    5 GA cWW 
No need to probe because of interaction between a=4LVW|1|A|C|85 B=4LVW|1|A|G|4
  5 Basepair    85    4 CG cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:   5  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   6   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LVW|1|A|G|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LVW|1|A|U|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LVW|1|A|A|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LVW|1|A|G|9
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LVW|1|A|U|77
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LVW|1|A|C|83
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LVW|1|A|C|82
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U77 - G9 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GCAUCC'
           RightLetter: 'GUA'
               Comment: ' // Basepair G78 - A8 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LVW|1|A|G|6'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LVW|1|A|U|7'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LVW|1|A|A|8'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LVW|1|A|G|9'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LVW|1|A|U|77'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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      JunctionDeletion: []
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                  lpar: []
                  rpar: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LVW|1|A|C|83'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
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               subtype: []
                  Left: []
                 Right: []
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                IBases: []
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                  lpar: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LVW|1|A|C|82'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
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                IBases: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 19
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G84 - A5 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 20
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C85 - G4 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 22
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 14
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 13
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 13
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 13
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 13
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 13
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 13
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 13
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 13
pMakeMotifModelFromSSF:  13   Initial Left  8 Right 13
pMakeMotifModelFromSSF:  14     Fixed Left  8 Right 13
pMakeMotifModelFromSSF:  15   Initial Left  8 Right 12
pMakeMotifModelFromSSF:  16     Fixed Left  8 Right 12
pMakeMotifModelFromSSF:  17   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  18  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  19  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  20   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 20
pNextNodeJunction: Found a hairpin at node 20

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_85630.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.5416

Timestamp 18-Jul-2025 22:48:55
pMakeSCFGModels: Making JAR3D model for motif group IL_85652.1, number 359 of 411
pMakeNodes starting loop:     a=1MFQ|1|A|U|181 B=1MFQ|1|A|A|216
  2 Basepair   181  216 UA cWW 
No need to probe because of interaction between a=1MFQ|1|A|G|182 B=1MFQ|1|A|A|215
  3 Basepair   182  215 GA tSH 
pMakeNodes probe for inserts:  a=1MFQ|1|A|A|183 B=1MFQ|1|A|A|214
    Insertion on left  1MFQ|1|A|A|183
    Insertion on left  1MFQ|1|A|A|184
    Insertion on left  1MFQ|1|A|C|185
    Insertion on left  1MFQ|1|A|C|186
    Insertion on right 1MFQ|1|A|A|214
    Insertion on right 1MFQ|1|A|A|213
pMakeNodesProbeForInsertions:  a 1MFQ|1|A|G|187 interacts with 1MFQ|1|A|C|212
pMakeNodesProbeForInsertions:  B 1MFQ|1|A|C|212 interacts with 1MFQ|1|A|G|187
pMakeNodesProbeForInsertions:  B 1MFQ|1|A|C|212 interacts with 1MFQ|1|A|G|187
pMakeNodes probed for insert:  a=1MFQ|1|A|G|187 B=1MFQ|1|A|C|212
  4 Basepair   187  212 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1MFQ|1|A|A|183
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1MFQ|1|A|A|184
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1MFQ|1|A|C|185
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1MFQ|1|A|C|186
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1MFQ|1|A|A|214
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1MFQ|1|A|A|213
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U181 - A216 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAACC'
           RightLetter: 'AAA'
               Comment: ' // Basepair G182 - A215 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1MFQ|1|A|A|183'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1MFQ|1|A|A|184'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1MFQ|1|A|C|185'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1MFQ|1|A|C|186'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1MFQ|1|A|A|214'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1MFQ|1|A|A|213'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 17
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G187 - C212 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 19
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 10
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:  13   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  14     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  15   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  16  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  17   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a hairpin at node 17

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_85652.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.5971

Timestamp 18-Jul-2025 22:48:55
pMakeSCFGModels: Making JAR3D model for motif group IL_85879.1, number 360 of 411
pMakeNodes starting loop:     a=8CRE|1|1|G|513 B=8CRE|1|1|C|571
  2 Basepair   513  571 GC cWW 
No need to probe because of interaction between a=8CRE|1|1|G|514 B=8CRE|1|1|A|570
  3 Basepair   514  570 GA cHW 
No need to probe because of interaction between a=8CRE|1|1|A|517 B=8CRE|1|1|U|569
  4 Basepair   517  569 AU tHW 
No need to probe because of interaction between a=8CRE|1|1|A|518 B=8CRE|1|1|A|568
  5 Basepair   518  568 AA tHW 
No need to probe because of interaction between a=8CRE|1|1|U|519 B=8CRE|1|1|G|567
  6 Basepair   519  567 UG tHW 
No need to probe because of interaction between a=8CRE|1|1|G|520 B=8CRE|1|1|C|566
  7 Basepair   520  566 GC cWW 
No need to probe because of interaction between a=8CRE|1|1|G|521 B=8CRE|1|1|A|565
  8 Basepair   521  565 GA cWW 
No need to probe because of interaction between a=8CRE|1|1|C|522 B=8CRE|1|1|G|564
  9 Basepair   522  564 CG cWW 
 10 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 15
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 14
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 13
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right 12
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G513 - C571 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G514 - A570 cHW '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A517 - U569 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A518 - A568 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U519 - G567 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G520 - C566 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G521 - A565 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C522 - G564 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 16
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 15
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 14
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 13
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right 12
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 10
pConsensusPairSubstitution:  New 4x4 substitution matrix for instance 1 of 1, pair 2,15 for nucleotide 2 (G) making self BPh with edge 1
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_85879.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -10.7851

Timestamp 18-Jul-2025 22:48:55
pMakeSCFGModels: Making JAR3D model for motif group IL_86012.1, number 361 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|U|1430 B=8P9A|1|sR|G|1278
pMakeNodes making a cluster near strand break a=8P9A|1|sR|U|1430 B=8P9A|1|sR|G|1278
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 6 and then 9 to 13
aa is 6 bb is 9
  2 Cluster   8P9A|1|sR|U|1430:8P9A|1|sR|U|1437 8P9A|1|sR|G|1273:8P9A|1|sR|G|1278
    LR Inter  8P9A|1|sR|C|1431 8P9A|1|sR|A|1275 tWH 
    LR Inter  8P9A|1|sR|U|1437 8P9A|1|sR|A|1275 cSW 
    LR Inter  8P9A|1|sR|A|1436 8P9A|1|sR|U|1276 cWW 
    LR Inter  8P9A|1|sR|U|1430 8P9A|1|sR|G|1278 cWW 
    LR Inter  8P9A|1|sR|G|1433 8P9A|1|sR|G|1278 tHS 
    RR Inter  8P9A|1|sR|G|1273 8P9A|1|sR|G|1277 cWH 
    Left  strand conserved insertion 8P9A|1|sR|U|1434 at position 4
pMakeNodesCluster a=7 B=8 at the end
pMakeNodesCluster a=7 B=8 at the end
No need to probe because of interaction between a=8P9A|1|sR|G|1438 B=8P9A|1|sR|U|1272
  3 Basepair  1438 1272 GU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6 Right  9 10 11 12 13
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 0 0 0 0 0 1 1 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5 6]
            RightIndex: [9 10 11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UCGUAU'
           RightLetter: 'GAUGG'
               Comment: ' // Cluster node 8P9A|1|sR|U|1430:8P9A|1|sR|U|1437 and 8P9A|1|sR|G|1273:8P9A|1|sR|G|1278'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: [1 2 3 4 5]
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
          LeftNotInter: 4
         RightNotInter: [1×0 double]
              NormCons: 0.1361
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1438 - U1272 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5  6 Right  9 10 11 12 13
pMakeMotifModelFromSSF:   3   Initial Left  7 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_86012.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2480

Timestamp 18-Jul-2025 22:48:55
pMakeSCFGModels: Making JAR3D model for motif group IL_86136.1, number 362 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|C|534 B=8CRE|1|CM|G|514
  2 Basepair   534  514 CG cWW 
No need to probe because of interaction between a=8CRE|1|CM|G|535 B=8CRE|1|CM|A|513
  3 Basepair   535  513 GA tSH 
pMakeNodes probe for inserts:  a=8CRE|1|CM|A|536 B=8CRE|1|CM|G|512
    Insertion on left  8CRE|1|CM|A|536
    Insertion on left  8CRE|1|CM|G|537
    Insertion on left  8CRE|1|CM|G|538
    Insertion on left  8CRE|1|CM|A|539
    Insertion on left  8CRE|1|CM|A|540
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|C|541 interacts with 8CRE|1|CM|G|512
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|512 interacts with 8CRE|1|CM|C|541
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|512 interacts with 8CRE|1|CM|C|541
pMakeNodes probed for insert:  a=8CRE|1|CM|C|541 B=8CRE|1|CM|G|512
  4 Basepair   541  512 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|G|514
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|C|534
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|G|535
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|A|536
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|G|537
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C534 - G514 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAGGAA'
           RightLetter: 'A'
               Comment: ' // Basepair G535 - A513 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|G|514'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|C|534'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|G|535'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|A|536'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|G|537'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C541 - G512 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:   9   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right  9
pMakeMotifModelFromSSF:  11   Initial Left  7 Right  9
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right  9
pMakeMotifModelFromSSF:  13   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  15   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a hairpin at node 15

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_86136.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.5775

Timestamp 18-Jul-2025 22:48:55
pMakeSCFGModels: Making JAR3D model for motif group IL_87211.1, number 363 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|1582 B=5J7L|1|DA|G|1416
pMakeNodes making a cluster near strand break a=5J7L|1|DA|C|1582 B=5J7L|1|DA|G|1416
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 3 and then 7 to 7
aa is 3 bb is 7
  2 Cluster   5J7L|1|DA|C|1582:5J7L|1|DA|C|1585 5J7L|1|DA|G|1416:5J7L|1|DA|G|1416
    LR Inter  5J7L|1|DA|C|1582 5J7L|1|DA|G|1416 cWW 
    LL Inter  5J7L|1|DA|C|1582 5J7L|1|DA|C|1585 cSW 
    Left  strand conserved insertion 5J7L|1|DA|A|1583 at position 2
pMakeNodesCluster a=4 B=6 at the end
pMakeNodesCluster a=4 B=6 at the end
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|1586 B=5J7L|1|DA|U|1415
    Insertion on left  5J7L|1|DA|A|1586
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|G|1587 interacts with 5J7L|1|DA|U|1415
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|U|1415 interacts with 5J7L|1|DA|G|1587
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|U|1415 interacts with 5J7L|1|DA|G|1587
  3 Initial   1586 (1 insertion) and 1415 (0 insertion)
pMakeNodes probed for insert:  a=5J7L|1|DA|G|1587 B=5J7L|1|DA|U|1415
  4 Basepair  1587 1415 GU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  7
pMakeMotifModelFromSSF:   3   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|1583
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 0 0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3]
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CAC'
           RightLetter: 'G'
               Comment: ' // Cluster node 5J7L|1|DA|C|1582:5J7L|1|DA|C|1585 and 5J7L|1|DA|G|1416:5J7L|1|DA|G|1416'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.2514
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|A|1586 - 5J7L|1|DA|U|1415 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|1583'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1587 - U1415 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3 Right  7
pMakeMotifModelFromSSF:   3   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   4     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  5 Right  6
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_87211.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.7096

Timestamp 18-Jul-2025 22:48:56
pMakeSCFGModels: Making JAR3D model for motif group IL_87284.1, number 364 of 411
pMakeNodes starting loop:     a=1KD4|1|A|U|3 B=1KD4|1|B|G|8
  2 Basepair     3    8 UG cWW 
No need to probe because of interaction between a=1KD4|1|A|C|4 B=1KD4|1|B|A|7
  3 Basepair     4    7 CA tSH 
No need to probe because of interaction between a=1KD4|1|A|A|5 B=1KD4|1|B|C|6
  4 Basepair     5    6 AC tHW 
No need to probe because of interaction between a=1KD4|1|A|C|6 B=1KD4|1|B|A|5
  5 Basepair     6    5 CA tWH 
No need to probe because of interaction between a=1KD4|1|A|A|7 B=1KD4|1|B|C|4
  6 Basepair     7    4 AC tHS 
No need to probe because of interaction between a=1KD4|1|A|G|8 B=1KD4|1|B|U|3
  7 Basepair     8    3 GU cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U3 - G8 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C4 - A7 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A5 - C6 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'A'
               Comment: ' // Basepair C6 - A5 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A7 - C4 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G8 - U3 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_87284.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.0745
   -9.0745
  -12.1567

Timestamp 18-Jul-2025 22:48:56
pMakeSCFGModels: Making JAR3D model for motif group IL_87290.1, number 365 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|2160 B=5J7L|1|DA|G|2128
  2 Basepair  2160 2128 CG cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|C|2161 B=5J7L|1|DA|G|2125
    Insertion on left  5J7L|1|DA|C|2161
    Insertion on left  5J7L|1|DA|G|2162
    Insertion on left  5J7L|1|DA|C|2164
    Insertion on left  5J7L|1|DA|U|2166
    Insertion on left  5J7L|1|DA|U|2167
    Insertion on left  5J7L|1|DA|G|2168
    Insertion on left  5J7L|1|DA|A|2169
    Insertion on left  5J7L|1|DA|A|2170
    Insertion on left  5J7L|1|DA|A|2171
    Insertion on left  5J7L|1|DA|A|2173
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|C|2174 interacts with 5J7L|1|DA|G|2125
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|2125 interacts with 5J7L|1|DA|C|2174
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|G|2125 interacts with 5J7L|1|DA|C|2174
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5J7L|1|DA|C|2174 B=5J7L|1|DA|G|2125
pMakeNodes making a cluster near strand break a=5J7L|1|DA|C|2174 B=5J7L|1|DA|G|2125
pMakeNodesCluster: amax is 12 bmin is 13, use_amax is 1
pMakeNodesCluster: Cluster goes from 12 to 12 and then 13 to 14
aa is 12 bb is 13
  3 Cluster   5J7L|1|DA|C|2174:5J7L|1|DA|C|2174 5J7L|1|DA|G|2124:5J7L|1|DA|G|2125
    LR Inter  5J7L|1|DA|C|2174 5J7L|1|DA|G|2124 cWW 
    LR Inter  5J7L|1|DA|C|2174 5J7L|1|DA|G|2125 cWS 
pMakeNodesCluster a=13 B=12 at the end
pMakeNodesCluster a=13 B=12 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3   Cluster Left 12 Right 13 14
pMakeMotifModelFromSSF:   4   Hairpin Left 13 Right 12
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2125
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|2126
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2127
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2128
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|2160
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|2161
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|G|2162
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|2163
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|2164
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|C|2165
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [15×15 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-11 8.1893e-10 8.1893e-09 8.1893e-08 8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 … ]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CCGCUUGAAAA'
           RightLetter: 'G'
               Comment: ' // Basepair C2160 - G2128 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|G|2125'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2]
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2561

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
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Node 6

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Node 7

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Node 8

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Node 9

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Node 10

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Node 11

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 12

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
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           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
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         Extensibility: []
                Delete: []
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                     Z: []
           MiddleIndex: []
                     P: []
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Node 13

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 14

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: []
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         Extensibility: []
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                     Z: []
           MiddleIndex: []
                     P: []
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Node 15

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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Node 16

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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           RightLetter: []
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Node 17

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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           RightLetter: ''
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              NumLoops: []
                  Edge: []
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                Delete: 1.0000e-03
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                     Z: []
           MiddleIndex: []
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Node 18

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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           RightLetter: []
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Node 19

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 20
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Node 20

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 11
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        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             LeftIndex: 11
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|C|2165'
              NumLoops: []
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                     Z: []
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Node 22

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 23
             LeftIndex: 12
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
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         Extensibility: []
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                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 23

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  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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             Insertion: []
                    id: []
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               Comment: ' // Cluster node 5J7L|1|DA|C|2174:5J7L|1|DA|C|2174 and 5J7L|1|DA|G|2124:5J7L|1|DA|G|2125'
              NumLoops: []
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                     Z: []
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Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 25
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
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           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
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Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

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              nextnode: 27
             LeftIndex: 13
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
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           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 13
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 15
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 15
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 14
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 14
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 14
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 14
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 14
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 14
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 14
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 14
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 14
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 14
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 14
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 14
pMakeMotifModelFromSSF:  15     Fixed Left  8 Right 14
pMakeMotifModelFromSSF:  16   Initial Left  9 Right 14
pMakeMotifModelFromSSF:  17     Fixed Left  9 Right 14
pMakeMotifModelFromSSF:  18   Initial Left 10 Right 14
pMakeMotifModelFromSSF:  19     Fixed Left 10 Right 14
pMakeMotifModelFromSSF:  20   Initial Left 11 Right 14
pMakeMotifModelFromSSF:  21     Fixed Left 11 Right 14
pMakeMotifModelFromSSF:  22   Initial Left 12 Right 14
pMakeMotifModelFromSSF:  23   Cluster Left 12 Right 13 14
pMakeMotifModelFromSSF:  24   Initial Left 13 Right 12
pMakeMotifModelFromSSF:  25   Hairpin Left 13 Right 12
pNextNodeJunction: Found a hairpin at node 25
pUpdateModelWithSSF: IL_87290.1 allow insertions from initial node 24?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 25

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_87290.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -13.4677

Timestamp 18-Jul-2025 22:48:56
pMakeSCFGModels: Making JAR3D model for motif group IL_87907.2, number 366 of 411
pMakeNodes starting loop:     a=6OL3|1|C|G|53 B=6OL3|1|C|C|80
  2 Basepair    53   80 GC cWW 
No need to probe because of interaction between a=6OL3|1|C|A|54 B=6OL3|1|C|C|79
  3 Basepair    54   79 AC cWW 
No need to probe because of interaction between a=6OL3|1|C|C|55 B=6OL3|1|C|G|78
  4 Basepair    55   78 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G53 - C80 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A54 - C79 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C55 - G78 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_87907.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.2523
   -4.7465
   -4.7465
   -4.7465
   -4.7465
   -4.0146
   -4.1113
   -4.2523
   -5.7817
   -3.7634
   -4.1113
   -3.7634
   -4.7965
   -4.1113
   -5.2376
   -4.4177
   -6.0079
   -3.7634
   -4.7965
   -4.4177
   -3.7634
   -5.1600
   -4.4177
   -3.7634
   -3.7634
   -5.2376
   -3.7634
   -3.7634
   -3.7634
   -4.1113
   -4.0146
   -5.9154
   -3.7634
   -5.7701
   -3.7634
   -5.9485
   -4.7434
   -3.8735
   -5.7701
   -4.1422
   -4.4177
   -5.0497
   -5.2376
   -3.7634
   -4.0146
   -3.7634
   -3.7634
   -3.7634
   -3.7634
   -4.0146
   -3.7634
   -5.7817
   -4.7965
   -5.1497
   -5.1497
   -4.1422
   -4.1113
   -3.7634
   -3.7634
   -4.4177
   -4.1422
   -4.1113
   -3.7634
   -5.7817
   -6.7939
   -4.4177
   -8.3509
   -4.4177
   -3.7634
   -6.2894
   -3.7634
   -6.1983
   -3.7634
   -4.7965
   -5.9463
   -3.7634
   -3.7634
   -6.4884
   -4.7434
   -4.1422
   -4.1422
   -6.6028
   -8.3509
   -5.9463
   -5.7564
   -4.7078
   -7.5832
   -5.2376
   -4.1422
   -3.8735
   -4.1422
   -6.9650
   -5.0866
   -4.7078
   -4.5056
   -5.2376
   -5.0866
   -4.7434
   -4.2523
   -4.7078
   -4.1422
   -4.1422
   -7.5832
   -5.2376
   -5.3399
   -6.6028
   -4.1422
   -4.7078
   -5.8052
   -4.2523
   -5.6218
   -5.5898
   -4.7078
   -6.0719
   -4.1422
   -4.7078
   -4.7078
   -4.9222
   -5.2376
   -4.1422
   -5.2376
   -4.7078
   -6.9833
   -6.4884
   -4.7965
   -4.8563
   -6.1129
   -6.4595
   -4.1422
   -9.7712
   -9.5958
   -5.8276
   -6.3894
   -6.5205
   -5.8276
   -6.1171
   -9.7712
   -5.3062
   -6.9833
   -5.8052
   -6.1171
   -4.7078
   -4.8563
   -5.6140
   -4.2523
   -5.3062
   -5.3062
   -5.3505
   -4.4177
   -5.2430
   -4.8563
   -5.6140
   -6.0719
   -6.4595
   -4.8563
   -5.3474
   -6.2461
   -9.7514
   -9.7514
   -6.1129
   -4.6185
   -7.4086
   -5.6140
   -6.5205
   -6.3741
   -5.2430
   -4.1422
   -5.3505
   -6.2461
   -5.4472
   -7.9995
   -6.3741
   -7.6532
   -5.1497
   -5.0684
  -10.4449
   -7.6620
   -7.7955
  -11.2105

Timestamp 18-Jul-2025 22:48:57
pMakeSCFGModels: Making JAR3D model for motif group IL_88017.1, number 367 of 411
pMakeNodes starting loop:     a=7JRT|1|A|G|24 B=7JRT|1|A|C|51
  2 Basepair    24   51 GC cWW 
pMakeNodes probe for inserts:  a=7JRT|1|A|A|25 B=7JRT|1|A|G|50
    Insertion on left  7JRT|1|A|A|25
    Insertion on left  7JRT|1|A|A|26
    Insertion on left  7JRT|1|A|C|27
    Insertion on left  7JRT|1|A|U|28
    Insertion on left  7JRT|1|A|A|29
pMakeNodesProbeForInsertions:  a 7JRT|1|A|C|30 interacts with 7JRT|1|A|G|50
pMakeNodesProbeForInsertions:  B 7JRT|1|A|G|50 interacts with 7JRT|1|A|C|30
pMakeNodesProbeForInsertions:  B 7JRT|1|A|G|50 interacts with 7JRT|1|A|C|30
pMakeNodes probed for insert:  a=7JRT|1|A|C|30 B=7JRT|1|A|G|50
  3 Basepair    30   50 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   4   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|A|25
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|A|26
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|C|27
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|U|28
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|A|29
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAACUA'
           RightLetter: 'C'
               Comment: ' // Basepair G24 - C51 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|A|25'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|A|26'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|C|27'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|U|28'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|A|29'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C30 - G50 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  12   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  13  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  14   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_88017.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.6289
   -2.6289
   -2.6289
   -2.6289
   -2.6289
   -2.6289
   -2.6289

Timestamp 18-Jul-2025 22:48:57
pMakeSCFGModels: Making JAR3D model for motif group IL_88072.1, number 368 of 411
pMakeNodes starting loop:     a=4FRG|1|B|A|6 B=4FRG|1|B|U|78
  2 Basepair     6   78 AU cWW 
pMakeNodes probe for inserts:  a=4FRG|1|B|A|7 B=4FRG|1|B|C|77
    Insertion on left  4FRG|1|B|A|7
    Insertion on left  4FRG|1|B|A|8
pMakeNodesProbeForInsertions:  a 4FRG|1|B|A|9 interacts with 4FRG|1|B|U|13
pMakeNodesProbeForInsertions:  B 4FRG|1|B|C|77 interacts with 4FRG|1|B|A|14
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but a makes a more important one
pMakeNodesProbeForInsertions:  B 4FRG|1|B|C|77 interacts with 4FRG|1|B|A|14
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4FRG|1|B|A|9 B=4FRG|1|B|C|77
pMakeNodes making a cluster near strand break a=4FRG|1|B|A|9 B=4FRG|1|B|C|77
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 9 and then 12 to 12
aa is 9 bb is 12
  3 Cluster   4FRG|1|B|A|9:4FRG|1|B|A|14 4FRG|1|B|C|77:4FRG|1|B|C|77
    LR Inter  4FRG|1|B|A|14 4FRG|1|B|C|77 bif 
    LL Inter  4FRG|1|B|A|9 4FRG|1|B|U|13 tWW 
    Left  strand conserved insertion 4FRG|1|B|G|10 at position 2
    Left  strand conserved insertion 4FRG|1|B|C|11 at position 3
    Left  strand conserved insertion 4FRG|1|B|A|12 at position 4
pMakeNodesCluster a=10 B=11 at the end
pMakeNodesCluster a=10 B=11 at the end
No need to probe because of interaction between a=4FRG|1|B|G|15 B=4FRG|1|B|C|76
  4 Basepair    15   76 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3   Cluster Left  4  5  6  7  8  9 Right 12
pMakeMotifModelFromSSF:   4  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   5   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4FRG|1|B|A|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4FRG|1|B|A|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAA'
           RightLetter: 'U'
               Comment: ' // Basepair A6 - U78 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4FRG|1|B|A|7'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4FRG|1|B|A|8'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [4 5 6 7 8 9]
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AGCAUA'
           RightLetter: 'C'
               Comment: ' // Cluster node 4FRG|1|B|A|9:4FRG|1|B|A|14 and 4FRG|1|B|C|77:4FRG|1|B|C|77'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5 6]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 1.0000

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G15 - C76 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 13
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 12
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   7   Cluster Left  4  5  6  7  8  9 Right 12
pMakeMotifModelFromSSF:   8   Initial Left 10 Right 11
pMakeMotifModelFromSSF:   9  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  10   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_88072.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.9414

Timestamp 18-Jul-2025 22:48:58
pMakeSCFGModels: Making JAR3D model for motif group IL_88082.1, number 369 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|G|42 B=8P9A|1|sR|C|433
  2 Basepair    42  433 GC cWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|A|43 B=8P9A|1|sR|G|432
    Insertion on left  8P9A|1|sR|A|43
    Insertion on left  8P9A|1|sR|U|44
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|A|46 interacts with 8P9A|1|sR|G|432
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|G|432 interacts with 8P9A|1|sR|A|46
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|G|432 interacts with 8P9A|1|sR|A|46
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|sR|A|46 B=8P9A|1|sR|G|432
  3 Basepair    46  432 AG tSS 
No need to probe because of interaction between a=8P9A|1|sR|G|48 B=8P9A|1|sR|C|431
  4 Basepair    48  431 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|A|43
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|U|44
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAU'
           RightLetter: 'C'
               Comment: ' // Basepair G42 - C433 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|A|43'
              NumLoops: []
                  Edge: 12
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|U|44'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A46 - G432 tSS '
              NumLoops: []
                  Edge: 12
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G48 - C431 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_88082.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.5137
   -6.5137

Timestamp 18-Jul-2025 22:48:58
pMakeSCFGModels: Making JAR3D model for motif group IL_88116.2, number 370 of 411
pMakeNodes starting loop:     a=8P9A|1|AR|U|2211 B=8P9A|1|AR|G|2234
  2 Basepair  2211 2234 UG cWW 
No need to probe because of interaction between a=8P9A|1|AR|C|2212 B=8P9A|1|AR|A|2233
  3 Basepair  2212 2233 CA tSH 
pMakeNodes probe for inserts:  a=8P9A|1|AR|A|2213 B=8P9A|1|AR|A|2232
    Insertion on left  8P9A|1|AR|A|2213
    Insertion on left  8P9A|1|AR|A|2214
    Insertion on left  8P9A|1|AR|A|2215
    Insertion on right 8P9A|1|AR|A|2232
    Insertion on right 8P9A|1|AR|C|2231
    Insertion on right 8P9A|1|AR|C|2230
pMakeNodesProbeForInsertions:  a 8P9A|1|AR|G|2216 interacts with 8P9A|1|AR|A|2229
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|A|2229 interacts with 8P9A|1|AR|G|2216
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8P9A|1|AR|A|2229 interacts with 8P9A|1|AR|G|2216
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|AR|G|2216 B=8P9A|1|AR|A|2229
  4 Basepair  2216 2229 GA cWW 
No need to probe because of interaction between a=8P9A|1|AR|U|2217 B=8P9A|1|AR|A|2228
  5 Basepair  2217 2228 UA cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|A|2213
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|A|2214
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|AR|A|2215
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|A|2232
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|C|2231
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|AR|C|2230
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U2211 - G2234 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAAA'
           RightLetter: 'CCAA'
               Comment: ' // Basepair C2212 - A2233 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|A|2213'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|A|2214'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|AR|A|2215'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|A|2232'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|C|2231'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|AR|C|2230'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 17
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G2216 - A2229 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 18
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U2217 - A2228 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 20
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 14
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 13
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 12
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 12
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 12
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 12
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 12
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 12
pMakeMotifModelFromSSF:  11   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  12     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  13   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  14     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  15   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  16  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  17  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  18   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 18
pNextNodeJunction: Found a hairpin at node 18

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_88116.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.5392
   -8.5392
   -9.9489

Timestamp 18-Jul-2025 22:48:58
pMakeSCFGModels: Making JAR3D model for motif group IL_88269.4, number 371 of 411
pMakeNodes starting loop:     a=4LFB|1|A|C|483 B=4LFB|1|A|G|450
  2 Basepair   483  450 CG cWW 
No need to probe because of interaction between a=4LFB|1|A|G|484 B=4LFB|1|A|C|449
  3 Basepair   484  449 GC tWW 
pMakeNodes probe for inserts:  a=4LFB|1|A|G|485 B=4LFB|1|A|A|448
pMakeNodesProbeForInsertions:  a 4LFB|1|A|G|485 interacts with 4LFB|1|A|U|486
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|448 interacts with 4LFB|1|A|U|486
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 4LFB|1|A|A|448 interacts with 4LFB|1|A|U|486
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4LFB|1|A|G|485 B=4LFB|1|A|A|448
pMakeNodes making a cluster near strand break a=4LFB|1|A|G|485 B=4LFB|1|A|A|448
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 4 and then 9 to 9
aa is 4 bb is 9
  4 Cluster   4LFB|1|A|G|485:4LFB|1|A|U|486 4LFB|1|A|A|448:4LFB|1|A|A|448
    LR Inter  4LFB|1|A|U|486 4LFB|1|A|A|448 tWH 
    LL Inter  4LFB|1|A|G|485 4LFB|1|A|U|486 cSH 
pMakeNodesCluster a=5 B=8 at the end
pMakeNodesCluster a=5 B=8 at the end
No need to probe because of interaction between a=4LFB|1|A|A|487 B=4LFB|1|A|G|447
  5 Basepair   487  447 AG tHS 
No need to probe because of interaction between a=4LFB|1|A|C|488 B=4LFB|1|A|G|446
  6 Basepair   488  446 CG cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4   Cluster Left  3  4 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C483 - G450 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G484 - C449 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4]
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 4LFB|1|A|G|485:4LFB|1|A|U|486 and 4LFB|1|A|A|448:4LFB|1|A|A|448'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A487 - G447 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C488 - G446 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4   Cluster Left  3  4 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_88269.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.2153
   -8.1991
   -7.6416

Timestamp 18-Jul-2025 22:48:58
pMakeSCFGModels: Making JAR3D model for motif group IL_88974.1, number 372 of 411
pMakeNodes starting loop:     a=7JRT|1|A|U|77 B=7JRT|1|A|A|125
  2 Basepair    77  125 UA cWW 
pMakeNodes probe for inserts:  a=7JRT|1|A|G|79 B=7JRT|1|A|G|124
    Insertion on left  7JRT|1|A|G|79
    Insertion on left  7JRT|1|A|C|80
    Insertion on left  7JRT|1|A|G|81
    Insertion on left  7JRT|1|A|A|82
    Insertion on left  7JRT|1|A|G|83
    Insertion on left  7JRT|1|A|C|84
pMakeNodesProbeForInsertions:  a 7JRT|1|A|A|85 interacts with 7JRT|1|A|G|124
pMakeNodesProbeForInsertions:  B 7JRT|1|A|G|124 interacts with 7JRT|1|A|A|85
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 7JRT|1|A|G|124 interacts with 7JRT|1|A|A|85
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=7JRT|1|A|A|85 B=7JRT|1|A|G|124
  3 Basepair    85  124 AG cWW 
No need to probe because of interaction between a=7JRT|1|A|C|86 B=7JRT|1|A|G|123
  4 Basepair    86  123 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   5   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|C|78
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|G|79
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|C|80
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|G|81
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|A|82
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7JRT|1|A|G|83
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-07 8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGCGAGC'
           RightLetter: 'A'
               Comment: ' // Basepair U77 - A125 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|C|78'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|G|79'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|C|80'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|G|81'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|A|82'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7JRT|1|A|G|83'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 16
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A85 - G124 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 17
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C86 - G123 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 11
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 11
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 11
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 11
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 11
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 11
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 11
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 11
pMakeMotifModelFromSSF:  12   Initial Left  7 Right 11
pMakeMotifModelFromSSF:  13     Fixed Left  7 Right 11
pMakeMotifModelFromSSF:  14   Initial Left  8 Right 11
pMakeMotifModelFromSSF:  15  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  16  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  17   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 17
pNextNodeJunction: Found a hairpin at node 17

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_88974.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.2458
   -7.2458

Timestamp 18-Jul-2025 22:48:58
pMakeSCFGModels: Making JAR3D model for motif group IL_89021.2, number 373 of 411
pMakeNodes starting loop:     a=4WF9|1|X|C|1388 B=4WF9|1|X|G|1417
  2 Basepair  1388 1417 CG cWW 
No need to probe because of interaction between a=4WF9|1|X|U|1389 B=4WF9|1|X|U|1416
pMakeNodes making a cluster near strand break a=4WF9|1|X|U|1389 B=4WF9|1|X|U|1416
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 2 and then 8 to 9
aa is 2 bb is 8
  3 Cluster   4WF9|1|X|U|1389:4WF9|1|X|U|1389 4WF9|1|X|A|1415:4WF9|1|X|U|1416
    LR Inter  4WF9|1|X|U|1389 4WF9|1|X|A|1415 tWH 
    LR Inter  4WF9|1|X|U|1389 4WF9|1|X|U|1416 tSH 
pMakeNodesCluster a=3 B=7 at the end
pMakeNodesCluster a=3 B=7 at the end
pMakeNodes probe for inserts:  a=4WF9|1|X|A|1390 B=4WF9|1|X|G|1414
    Insertion on left  4WF9|1|X|A|1390
pMakeNodesProbeForInsertions:  a 4WF9|1|X|A|1391 interacts with 4WF9|1|X|G|1414
pMakeNodesProbeForInsertions:  B 4WF9|1|X|G|1414 interacts with 4WF9|1|X|A|1391
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4WF9|1|X|G|1414 interacts with 4WF9|1|X|A|1391
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  4 Initial   1390 (1 insertion) and 1414 (0 insertion)
pMakeNodes probed for insert:  a=4WF9|1|X|A|1391 B=4WF9|1|X|G|1414
  5 Basepair  1391 1414 AG tHS 
No need to probe because of interaction between a=4WF9|1|X|G|1392 B=4WF9|1|X|C|1413
  6 Basepair  1392 1413 GC cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  2 Right  8  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|A|1390
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1388 - G1417 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: 2
            RightIndex: [8 9]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'U'
           RightLetter: 'AU'
               Comment: ' // Cluster node 4WF9|1|X|U|1389:4WF9|1|X|U|1389 and 4WF9|1|X|A|1415:4WF9|1|X|U|1416'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2]
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2500

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: []
               Comment: ' // Initial node 4WF9|1|X|A|1390 - 4WF9|1|X|G|1414 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|A|1390'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A1391 - G1414 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1392 - C1413 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3   Cluster Left  2 Right  8  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   8  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_89021.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.4807
   -6.4807
   -6.4807
   -6.7461
   -7.7279
   -6.0068

Timestamp 18-Jul-2025 22:48:59
pMakeSCFGModels: Making JAR3D model for motif group IL_89047.1, number 374 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|C|895 B=8CRE|1|CM|G|884
pMakeNodes making a cluster near strand break a=8CRE|1|CM|C|895 B=8CRE|1|CM|G|884
pMakeNodesCluster: amax is 9 bmin is 10, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 14 to 16
aa is 5 bb is 14
  2 Cluster   8CRE|1|CM|C|895:8CRE|1|CM|A|900 8CRE|1|CM|C|882:8CRE|1|CM|G|884
    LR Inter  8CRE|1|CM|A|900 8CRE|1|CM|C|882 tHS 
    LR Inter  8CRE|1|CM|C|895 8CRE|1|CM|G|884 cWW 
    LL Inter  8CRE|1|CM|C|895 8CRE|1|CM|A|900 cSS 
    Left  strand conserved insertion 8CRE|1|CM|U|896 at position 2
    Left  strand conserved insertion 8CRE|1|CM|U|897 at position 3
    Left  strand conserved insertion 8CRE|1|CM|G|899 at position 4
    Right strand conserved insertion 8CRE|1|CM|A|883 at position 2
pMakeNodesCluster a=6 B=13 at the end
pMakeNodesCluster a=6 B=13 at the end
pMakeNodes probe for inserts:  a=8CRE|1|CM|U|901 B=8CRE|1|CM|U|881
    Insertion on left  8CRE|1|CM|U|901
    Insertion on right 8CRE|1|CM|U|881
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|U|902 interacts with 8CRE|1|CM|G|880
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|880 interacts with 8CRE|1|CM|U|902
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|880 interacts with 8CRE|1|CM|U|902
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  3 Initial    901 (1 insertion) and  881 (1 insertion)
pMakeNodes probed for insert:  a=8CRE|1|CM|U|902 B=8CRE|1|CM|G|880
  4 Basepair   902  880 UG cSW 
No need to probe because of interaction between a=8CRE|1|CM|U|903 B=8CRE|1|CM|U|879
  5 Basepair   903  879 UU cWH 
No need to probe because of interaction between a=8CRE|1|CM|A|904 B=8CRE|1|CM|U|878
  6 Basepair   904  878 AU cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 14 15 16
pMakeMotifModelFromSSF:   3   Initial Left  6 Right 13
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:   6  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   7   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|A|883
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|CM|A|900
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 16
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [16×16 double]
         Extensibility: [0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: [14 15 16]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUUGA'
           RightLetter: 'CAG'
               Comment: ' // Cluster node 8CRE|1|CM|C|895:8CRE|1|CM|A|900 and 8CRE|1|CM|C|882:8CRE|1|CM|G|884'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×7 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [7×2 double]
    InteractionComment: {1×7 cell}
      JunctionDeletion: []
          InterIndices: [7×2 double]
          LeftNotInter: [2 3 4]
         RightNotInter: 2
              NormCons: 0.0719
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Initial node 8CRE|1|CM|U|901 - 8CRE|1|CM|U|881 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|A|883'
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|CM|A|900'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U902 - G880 cSW '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U903 - U879 cWH '
              NumLoops: []
                  Edge: 3
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A904 - U878 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 16
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 14 15 16
pMakeMotifModelFromSSF:   3   Initial Left  6 Right 13
pMakeMotifModelFromSSF:   4     Fixed Left  6 Right 13
pMakeMotifModelFromSSF:   5   Initial Left  7 Right 13
pMakeMotifModelFromSSF:   6     Fixed Left  7 Right 13
pMakeMotifModelFromSSF:   7   Initial Left  7 Right 12
pMakeMotifModelFromSSF:   8  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  11   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_89047.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.7224

Timestamp 18-Jul-2025 22:48:59
pMakeSCFGModels: Making JAR3D model for motif group IL_89099.1, number 375 of 411
pMakeNodes starting loop:     a=1D4R|1|A|G|12 B=1D4R|1|B|C|17
  2 Basepair    12   17 GC cWW 
No need to probe because of interaction between a=1D4R|1|A|G|13 B=1D4R|1|B|G|16
  3 Basepair    13   16 GG bif 
No need to probe because of interaction between a=1D4R|1|A|G|14 B=1D4R|1|B|A|15
  4 Basepair    14   15 GA wat 
No need to probe because of interaction between a=1D4R|1|A|A|15 B=1D4R|1|B|G|14
  5 Basepair    15   14 AG wat 
No need to probe because of interaction between a=1D4R|1|A|G|16 B=1D4R|1|B|G|13
  6 Basepair    16   13 GG bif 
No need to probe because of interaction between a=1D4R|1|A|C|17 B=1D4R|1|B|G|12
  7 Basepair    17   12 CG cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G12 - C17 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G13 - G16 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G14 - A15 wat '
              NumLoops: []
                  Edge: 14
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A15 - G14 wat '
              NumLoops: []
                  Edge: 14
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G16 - G13 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C17 - G12 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 12
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   8   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_89099.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7275

Timestamp 18-Jul-2025 22:48:59
pMakeSCFGModels: Making JAR3D model for motif group IL_89312.1, number 376 of 411
pMakeNodes starting loop:     a=3IGI|1|A|U|103 B=3IGI|1|A|G|79
  2 Basepair   103   79 UG cWW 
No need to probe because of interaction between a=3IGI|1|A|G|104 B=3IGI|1|A|A|78
  3 Basepair   104   78 GA tSH 
pMakeNodes probe for inserts:  a=3IGI|1|A|G|108 B=3IGI|1|A|A|77
    Insertion on left  3IGI|1|A|G|108
pMakeNodesProbeForInsertions:  a 3IGI|1|A|A|109 interacts with 3IGI|1|A|A|77
pMakeNodesProbeForInsertions:  B 3IGI|1|A|A|77 interacts with 3IGI|1|A|A|109
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3IGI|1|A|A|77 interacts with 3IGI|1|A|A|109
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3IGI|1|A|A|109 B=3IGI|1|A|A|77
  4 Basepair   109   77 AA cWS 
pMakeNodes probe for inserts:  a=3IGI|1|A|A|110 B=3IGI|1|A|C|76
    Insertion on left  3IGI|1|A|A|110
pMakeNodesProbeForInsertions:  a 3IGI|1|A|G|111 interacts with 3IGI|1|A|C|76
pMakeNodesProbeForInsertions:  B 3IGI|1|A|C|76 interacts with 3IGI|1|A|G|111
pMakeNodesProbeForInsertions:  B 3IGI|1|A|C|76 interacts with 3IGI|1|A|G|111
pMakeNodes probed for insert:  a=3IGI|1|A|G|111 B=3IGI|1|A|C|76
  5 Basepair   111   76 GC cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|A|78
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|U|103
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U103 - G79 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GG'
           RightLetter: 'A'
               Comment: ' // Basepair G104 - A78 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IGI|1|A|A|78'
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'A'
               Comment: ' // Basepair A109 - A77 cWS '
              NumLoops: []
                  Edge: 5
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IGI|1|A|U|103'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G111 - C76 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  10   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_89312.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.1602

Timestamp 18-Jul-2025 22:48:59
pMakeSCFGModels: Making JAR3D model for motif group IL_89505.4, number 377 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|G|555 B=8CRE|1|CM|C|585
  2 Basepair   555  585 GC cWW 
pMakeNodes probe for inserts:  a=8CRE|1|CM|U|556 B=8CRE|1|CM|G|584
    Insertion on left  8CRE|1|CM|U|556
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|C|557 interacts with 8CRE|1|CM|G|584
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|584 interacts with 8CRE|1|CM|C|557
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|G|584 interacts with 8CRE|1|CM|C|557
pMakeNodes probed for insert:  a=8CRE|1|CM|C|557 B=8CRE|1|CM|G|584
  3 Basepair   557  584 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|U|556
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GU'
           RightLetter: 'C'
               Comment: ' // Basepair G555 - C585 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|U|556'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C557 - G584 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_89505.4_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -2.2793
   -2.2793
   -3.0650
   -2.8529
   -2.8529
   -2.1490
   -2.8529
   -2.1490
   -2.7865
   -3.2934
   -3.9309
   -2.1490
   -3.9309
   -2.1490
   -2.2793
   -3.1959
   -2.1490
   -3.4236
   -2.1490
   -2.2793
   -2.9347
   -2.1490
   -2.1490
   -2.1490
   -3.0650
   -3.0650
   -2.1490
   -2.2793
   -2.1490
   -2.9347
   -2.8529
   -3.8423
   -3.0650
   -2.1490
   -3.5722
   -2.8529
   -2.1490
   -2.7865
   -2.1490
   -4.1181
   -2.7865
   -2.2793
   -2.7865
   -3.1959
   -2.1490
   -4.1181
   -2.7865
   -2.1490
   -2.7865
   -3.5722
   -3.5722
   -2.7865
   -3.0650
   -3.3262
   -3.8423
   -3.0650
   -2.1490
   -3.0650
   -2.1490
   -2.2793
   -2.2793
   -2.8529
   -5.6810
   -2.9347
   -5.2624
   -5.2624
   -3.8423
   -2.1490
   -2.8529
   -2.8529
   -2.8529
   -2.1490
   -3.1959
   -3.1959
   -4.4158
   -3.4236
   -3.5722
   -3.7120
   -3.7120
   -3.1959
   -2.1490
   -2.2793
   -3.6386
   -2.2793
   -2.2793
   -2.2793
   -2.2793
   -2.2793
   -2.2793
   -2.2793
   -2.2793
   -2.9347
   -2.1490
   -2.2793
   -3.6386
   -3.6386
   -2.7865
   -2.2793
   -3.7120
   -3.1959
   -2.1490
   -2.1490
   -3.8423
   -2.7865
   -3.8423
   -3.8423
   -2.1490
   -3.1959
   -2.1490
   -2.1490
   -3.7120
   -2.9347
   -2.9347
   -3.1959
   -3.4236
   -3.3262
   -3.3262

Timestamp 18-Jul-2025 22:49:00
pMakeSCFGModels: Making JAR3D model for motif group IL_89984.3, number 378 of 411
pMakeNodes starting loop:     a=8SYK|1|A|G|12 B=8SYK|1|A|C|111
  2 Basepair    12  111 GC cWW 
pMakeNodes probe for inserts:  a=8SYK|1|A|U|13 B=8SYK|1|A|U|110
    Insertion on left  8SYK|1|A|U|13
    Insertion on left  8SYK|1|A|A|14
    Insertion on right 8SYK|1|A|U|110
pMakeNodesProbeForInsertions:  a 8SYK|1|A|A|16 interacts with 8SYK|1|A|U|109
pMakeNodesProbeForInsertions:  B 8SYK|1|A|U|109 interacts with 8SYK|1|A|A|16
pMakeNodesProbeForInsertions:  B 8SYK|1|A|U|109 interacts with 8SYK|1|A|A|16
pMakeNodes probed for insert:  a=8SYK|1|A|A|16 B=8SYK|1|A|U|109
  3 Basepair    16  109 AU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8SYK|1|A|U|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8SYK|1|A|A|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8SYK|1|A|U|109
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUA'
           RightLetter: 'UC'
               Comment: ' // Basepair G12 - C111 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8SYK|1|A|U|13'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8SYK|1|A|A|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8SYK|1|A|U|109'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A16 - U109 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_89984.3_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.0144
   -5.0144

Timestamp 18-Jul-2025 22:49:00
pMakeSCFGModels: Making JAR3D model for motif group IL_90346.1, number 379 of 411
pMakeNodes starting loop:     a=7KVT|1|B|C|67 B=7KVT|1|B|G|50
  2 Basepair    67   50 CG cWW 
pMakeNodes probe for inserts:  a=7KVT|1|B|U|68 B=7KVT|1|B|A|49
    Insertion on left  7KVT|1|B|U|68
    Insertion on left  7KVT|1|B|A|69
    Insertion on left  7KVT|1|B|A|70
    Insertion on left  7KVT|1|B|G|71
    Insertion on right 7KVT|1|B|A|49
pMakeNodesProbeForInsertions:  a 7KVT|1|B|C|72 interacts with 7KVT|1|B|G|47
pMakeNodesProbeForInsertions:  B 7KVT|1|B|G|47 interacts with 7KVT|1|B|C|72
pMakeNodesProbeForInsertions:  B 7KVT|1|B|G|47 interacts with 7KVT|1|B|C|72
pMakeNodes probed for insert:  a=7KVT|1|B|C|72 B=7KVT|1|B|G|47
  3 Basepair    72   47 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7KVT|1|B|A|48
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7KVT|1|B|A|49
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7KVT|1|B|G|50
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 7KVT|1|B|C|67
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 7KVT|1|B|A|70
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CUAAG'
           RightLetter: 'AG'
               Comment: ' // Basepair C67 - G50 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7KVT|1|B|A|48'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7KVT|1|B|A|49'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7KVT|1|B|G|50'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 7KVT|1|B|C|67'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 7KVT|1|B|A|70'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C72 - G47 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  8
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  14   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 14
pNextNodeJunction: Found a hairpin at node 14

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_90346.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.9106

Timestamp 18-Jul-2025 22:49:00
pMakeSCFGModels: Making JAR3D model for motif group IL_90351.1, number 380 of 411
pMakeNodes starting loop:     a=2QEK|1|B|G|7 B=2QEK|1|A|C|17
pMakeNodes making a cluster near strand break a=2QEK|1|B|G|7 B=2QEK|1|A|C|17
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 7 to 7
aa is 2 bb is 7
  2 Cluster   2QEK|1|B|G|7:2QEK|1|B|A|8 2QEK|1|A|C|17:2QEK|1|A|C|17
    LR Inter  2QEK|1|B|G|7 2QEK|1|A|C|17 cWW 
    LR Inter  2QEK|1|B|A|8 2QEK|1|A|C|17 tHS 
pMakeNodesCluster a=3 B=6 at the end
pMakeNodesCluster a=3 B=6 at the end
No need to probe because of interaction between a=2QEK|1|B|A|9 B=2QEK|1|A|A|16
  3 Basepair     9   16 AA cWW 
No need to probe because of interaction between a=2QEK|1|B|G|10 B=2QEK|1|A|C|15
  4 Basepair    10   15 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GA'
           RightLetter: 'C'
               Comment: ' // Cluster node 2QEK|1|B|G|7:2QEK|1|B|A|8 and 2QEK|1|A|C|17:2QEK|1|A|C|17'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2516
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A9 - A16 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G10 - C15 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  7
pMakeMotifModelFromSSF:   3   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_90351.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.6455
   -5.6455
   -5.5754
   -8.8725
   -7.5305
   -7.2287
   -6.7222
   -7.4202

Timestamp 18-Jul-2025 22:49:00
pMakeSCFGModels: Making JAR3D model for motif group IL_90729.1, number 381 of 411
pMakeNodes starting loop:     a=4WF9|1|X|G|215 B=4WF9|1|X|C|187
  2 Basepair   215  187 GC cWW 
pMakeNodes probe for inserts:  a=4WF9|1|X|A|216 B=4WF9|1|X|C|186
    Insertion on left  4WF9|1|X|A|216
pMakeNodesProbeForInsertions:  a 4WF9|1|X|G|217 interacts with 4WF9|1|X|C|186
pMakeNodesProbeForInsertions:  B 4WF9|1|X|C|186 interacts with 4WF9|1|X|G|217
pMakeNodesProbeForInsertions:  B 4WF9|1|X|C|186 interacts with 4WF9|1|X|G|217
pMakeNodes probed for insert:  a=4WF9|1|X|G|217 B=4WF9|1|X|C|186
  3 Basepair   217  186 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4WF9|1|X|C|187
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'C'
               Comment: ' // Basepair G215 - C187 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4WF9|1|X|C|187'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G217 - C186 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  5
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  4
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   5  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   6   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_90729.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.2250
   -3.2250
   -3.2250
   -3.7365
   -3.6013
   -3.2250
   -3.2250
   -3.2250
   -3.5860
   -4.1849
   -3.5860
   -3.2250
   -3.2250
   -3.8239
   -3.2250
   -3.9623
   -5.9999
   -5.3671
   -3.8411
   -3.9623
   -4.1328
   -3.2250
   -5.6229
   -7.7297
   -4.1849
   -4.1849
   -3.8239
   -3.8239
   -6.0148
   -7.7098

Timestamp 18-Jul-2025 22:49:01
pMakeSCFGModels: Making JAR3D model for motif group IL_91592.1, number 382 of 411
pMakeNodes starting loop:     a=5U3G|1|B|C|60 B=5U3G|1|B|G|80
  2 Basepair    60   80 CG cWW 
pMakeNodes probe for inserts:  a=5U3G|1|B|A|61 B=5U3G|1|B|G|79
    Insertion on left  5U3G|1|B|A|61
    Insertion on left  5U3G|1|B|C|62
    Insertion on left  5U3G|1|B|G|63
    Insertion on left  5U3G|1|B|G|64
pMakeNodesProbeForInsertions:  a 5U3G|1|B|C|65 interacts with 5U3G|1|B|G|79
pMakeNodesProbeForInsertions:  B 5U3G|1|B|G|79 interacts with 5U3G|1|B|C|65
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5U3G|1|B|G|79 interacts with 5U3G|1|B|C|65
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5U3G|1|B|C|65 B=5U3G|1|B|G|79
  3 Basepair    65   79 CG tHH 
No need to probe because of interaction between a=5U3G|1|B|G|66 B=5U3G|1|B|C|78
  4 Basepair    66   78 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5U3G|1|B|A|61
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5U3G|1|B|C|62
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5U3G|1|B|G|63
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5U3G|1|B|G|64
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CACGG'
           RightLetter: 'G'
               Comment: ' // Basepair C60 - G80 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5U3G|1|B|A|61'
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5U3G|1|B|C|62'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5U3G|1|B|G|63'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5U3G|1|B|G|64'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C65 - G79 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G66 - C78 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 15
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  9
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  12  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  13   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 13
pNextNodeJunction: Found a hairpin at node 13

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_91592.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7044
   -6.1070

Timestamp 18-Jul-2025 22:49:01
pMakeSCFGModels: Making JAR3D model for motif group IL_91636.1, number 383 of 411
pMakeNodes starting loop:     a=3KTW|1|C|G|193 B=3KTW|1|C|C|227
  2 Basepair   193  227 GC cWW 
pMakeNodes probe for inserts:  a=3KTW|1|C|G|194 B=3KTW|1|C|G|226
    Insertion on left  3KTW|1|C|G|194
    Insertion on left  3KTW|1|C|G|195
    Insertion on right 3KTW|1|C|G|226
pMakeNodesProbeForInsertions:  a 3KTW|1|C|A|196 interacts with 3KTW|1|C|U|225
pMakeNodesProbeForInsertions:  B 3KTW|1|C|U|225 interacts with 3KTW|1|C|A|196
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3KTW|1|C|U|225 interacts with 3KTW|1|C|A|196
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3KTW|1|C|A|196 B=3KTW|1|C|U|225
  3 Basepair   196  225 AU tHW 
pMakeNodes probe for inserts:  a=3KTW|1|C|A|197 B=3KTW|1|C|G|224
    Insertion on left  3KTW|1|C|A|197
    Insertion on left  3KTW|1|C|C|198
pMakeNodesProbeForInsertions:  a 3KTW|1|C|C|199 interacts with 3KTW|1|C|G|224
pMakeNodesProbeForInsertions:  B 3KTW|1|C|G|224 interacts with 3KTW|1|C|C|199
pMakeNodesProbeForInsertions:  B 3KTW|1|C|G|224 interacts with 3KTW|1|C|C|199
pMakeNodes probed for insert:  a=3KTW|1|C|C|199 B=3KTW|1|C|G|224
  4 Basepair   199  224 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3KTW|1|C|G|194
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3KTW|1|C|G|195
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3KTW|1|C|G|226
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3KTW|1|C|A|197
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3KTW|1|C|C|198
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GGG'
           RightLetter: 'GC'
               Comment: ' // Basepair G193 - C227 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3KTW|1|C|G|194'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3KTW|1|C|G|195'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3KTW|1|C|G|226'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AAC'
           RightLetter: 'U'
               Comment: ' // Basepair A196 - U225 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3KTW|1|C|A|197'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3KTW|1|C|C|198'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C199 - G224 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 18
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  9
pMakeMotifModelFromSSF:  10     Fixed Left  5 Right  8
pMakeMotifModelFromSSF:  11   Initial Left  6 Right  8
pMakeMotifModelFromSSF:  12     Fixed Left  6 Right  8
pMakeMotifModelFromSSF:  13   Initial Left  7 Right  8
pMakeMotifModelFromSSF:  14  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  15   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a hairpin at node 15

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_91636.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.4438

Timestamp 18-Jul-2025 22:49:01
pMakeSCFGModels: Making JAR3D model for motif group IL_91698.1, number 384 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|U|1519 B=8P9A|1|sR|A|1487
  2 Basepair  1519 1487 UA cWW 
No need to probe because of interaction between a=8P9A|1|sR|U|1520 B=8P9A|1|sR|G|1486
  3 Basepair  1520 1486 UG tWW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|G|1521 B=8P9A|1|sR|C|1485
    Insertion on left  8P9A|1|sR|G|1521
    Insertion on left  8P9A|1|sR|U|1522
    Insertion on left  8P9A|1|sR|G|1523
    Insertion on left  8P9A|1|sR|A|1524
    Insertion on right 8P9A|1|sR|C|1485
    Insertion on right 8P9A|1|sR|G|1484
    Insertion on right 8P9A|1|sR|A|1483
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|A|1525 interacts with 8P9A|1|sR|C|1482
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|C|1482 interacts with 8P9A|1|sR|A|1525
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|C|1482 interacts with 8P9A|1|sR|A|1525
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=8P9A|1|sR|A|1525 B=8P9A|1|sR|C|1482
  4 Basepair  1525 1482 AC tHW 
pMakeNodes probe for inserts:  a=8P9A|1|sR|A|1526 B=8P9A|1|sR|C|1481
    Insertion on left  8P9A|1|sR|A|1526
    Insertion on right 8P9A|1|sR|C|1481
pMakeNodesProbeForInsertions:  a 8P9A|1|sR|C|1527 interacts with 8P9A|1|sR|G|1480
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|G|1480 interacts with 8P9A|1|sR|C|1527
pMakeNodesProbeForInsertions:  B 8P9A|1|sR|G|1480 interacts with 8P9A|1|sR|C|1527
pMakeNodes probed for insert:  a=8P9A|1|sR|C|1527 B=8P9A|1|sR|G|1480
  5 Basepair  1527 1480 CG cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:   5  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:   6   Hairpin Left 10 Right  9
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|C|1482
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|A|1483
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|G|1484
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|C|1485
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|A|1525
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|A|1524
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|G|1523
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8P9A|1|sR|A|1487
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8P9A|1|sR|G|1521
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [17×17 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1519 - A1487 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UGUGA'
           RightLetter: 'AGCG'
               Comment: ' // Basepair U1520 - G1486 tWW '
              NumLoops: []
                  Edge: 2
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|C|1482'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|A|1483'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|G|1484'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|C|1485'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 13
             LeftIndex: 7
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|A|1525'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|A|1524'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 16
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 17
             LeftIndex: 7
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|G|1523'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 18
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 19
             LeftIndex: 7
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: 'CC'
               Comment: ' // Basepair A1525 - C1482 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8P9A|1|sR|A|1487'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8P9A|1|sR|G|1521'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 24
             LeftIndex: 9
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1527 - G1480 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 27
             LeftIndex: 10
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 10
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 17
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 17
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 16
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right 15
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 15
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right 15
pMakeMotifModelFromSSF:   7   Initial Left  5 Right 15
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right 15
pMakeMotifModelFromSSF:   9   Initial Left  6 Right 15
pMakeMotifModelFromSSF:  10     Fixed Left  6 Right 15
pMakeMotifModelFromSSF:  11   Initial Left  7 Right 15
pMakeMotifModelFromSSF:  12     Fixed Left  7 Right 15
pMakeMotifModelFromSSF:  13   Initial Left  7 Right 14
pMakeMotifModelFromSSF:  14     Fixed Left  7 Right 14
pMakeMotifModelFromSSF:  15   Initial Left  7 Right 13
pMakeMotifModelFromSSF:  16     Fixed Left  7 Right 13
pMakeMotifModelFromSSF:  17   Initial Left  7 Right 12
pMakeMotifModelFromSSF:  18  Basepair Left  7 Right 12
pMakeMotifModelFromSSF:  19     Fixed Left  8 Right 11
pMakeMotifModelFromSSF:  20   Initial Left  9 Right 11
pMakeMotifModelFromSSF:  21     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:  22   Initial Left  9 Right 10
pMakeMotifModelFromSSF:  23  Basepair Left  9 Right 10
pMakeMotifModelFromSSF:  24   Hairpin Left 10 Right  9
pNextNodeJunction: Found a hairpin at node 24
pNextNodeJunction: Found a hairpin at node 24

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_91698.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7285
   -6.7285

Timestamp 18-Jul-2025 22:49:01
pMakeSCFGModels: Making JAR3D model for motif group IL_91920.1, number 385 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|G|1202 B=5J7L|1|DA|C|1243
  2 Basepair  1202 1243 GC cWW 
No need to probe because of interaction between a=5J7L|1|DA|U|1203 B=5J7L|1|DA|U|1242
  3 Basepair  1203 1242 UU cWW 
No need to probe because of interaction between a=5J7L|1|DA|A|1204 B=5J7L|1|DA|A|1241
  4 Basepair  1204 1241 AA tHH 
No need to probe because of interaction between a=5J7L|1|DA|G|1206 B=5J7L|1|DA|U|1240
  5 Basepair  1206 1240 GU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1202 - C1243 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'U'
               Comment: ' // Basepair U1203 - U1242 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A1204 - A1241 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1206 - U1240 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_91920.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.6055

Timestamp 18-Jul-2025 22:49:01
pMakeSCFGModels: Making JAR3D model for motif group IL_92446.2, number 386 of 411
pMakeNodes starting loop:     a=1MMS|1|C|C|1076 B=1MMS|1|C|G|1062
  2 Basepair  1076 1062 CG cWW 
pMakeNodes probe for inserts:  a=1MMS|1|C|A|1077 B=1MMS|1|C|U|1060
    Insertion on left  1MMS|1|C|A|1077
    Insertion on left  1MMS|1|C|U|1078
    Insertion on right 1MMS|1|C|U|1060
pMakeNodesProbeForInsertions:  a 1MMS|1|C|C|1079 interacts with 1MMS|1|C|G|1059
pMakeNodesProbeForInsertions:  B 1MMS|1|C|G|1059 interacts with 1MMS|1|C|C|1079
pMakeNodesProbeForInsertions:  B 1MMS|1|C|G|1059 interacts with 1MMS|1|C|C|1079
pMakeNodes probed for insert:  a=1MMS|1|C|C|1079 B=1MMS|1|C|G|1059
  3 Basepair  1079 1059 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1MMS|1|C|U|1060
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1MMS|1|C|U|1061
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1MMS|1|C|A|1077
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CAU'
           RightLetter: 'UG'
               Comment: ' // Basepair C1076 - G1062 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1MMS|1|C|U|1060'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1MMS|1|C|U|1061'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1MMS|1|C|A|1077'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1079 - G1059 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_92446.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.2259
   -4.2259
   -4.2259
   -6.5720
   -4.2259

Timestamp 18-Jul-2025 22:49:02
pMakeSCFGModels: Making JAR3D model for motif group IL_92634.2, number 387 of 411
pMakeNodes starting loop:     a=8CRE|1|1|A|143 B=8CRE|1|1|U|123
  2 Basepair   143  123 AU cWW 
pMakeNodes probe for inserts:  a=8CRE|1|1|G|144 B=8CRE|1|1|A|122
    Insertion on left  8CRE|1|1|G|144
    Insertion on left  8CRE|1|1|U|145
pMakeNodesProbeForInsertions:  a 8CRE|1|1|G|147 interacts with 8CRE|1|1|U|148
pMakeNodesProbeForInsertions:  B 8CRE|1|1|A|122 interacts with 8CRE|1|1|U|148
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8CRE|1|1|A|122 interacts with 8CRE|1|1|U|148
pMakeNodes probed for insert:  a=8CRE|1|1|G|147 B=8CRE|1|1|A|122
pMakeNodes making a cluster near strand break a=8CRE|1|1|G|147 B=8CRE|1|1|A|122
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 4 to 5 and then 6 to 6
aa is 5 bb is 6
  3 Cluster   8CRE|1|1|G|147:8CRE|1|1|U|148 8CRE|1|1|A|122:8CRE|1|1|A|122
    LR Inter  8CRE|1|1|U|148 8CRE|1|1|A|122 cWW 
    LL Inter  8CRE|1|1|G|147 8CRE|1|1|U|148 cSH 
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Cluster Left  4  5 Right  6
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|U|123
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|1|A|143
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AGU'
           RightLetter: 'U'
               Comment: ' // Basepair A143 - U123 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|U|123'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2555

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|1|A|143'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 8
             LeftIndex: [4 5]
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'A'
               Comment: ' // Cluster node 8CRE|1|1|G|147:8CRE|1|1|U|148 and 8CRE|1|1|A|122:8CRE|1|1|A|122'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2555

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7   Cluster Left  4  5 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   9   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 9
pUpdateModelWithSSF: IL_92634.2 allow insertions from initial node 8?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_92634.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.9771
   -3.9771
   -6.2337

Timestamp 18-Jul-2025 22:49:02
pMakeSCFGModels: Making JAR3D model for motif group IL_93889.1, number 388 of 411
pMakeNodes starting loop:     a=4MGN|1|A|U|81 B=4MGN|1|A|G|23
  2 Basepair    81   23 UG cWW 
No need to probe because of interaction between a=4MGN|1|A|G|82 B=4MGN|1|A|A|22
  3 Basepair    82   22 GA tSH 
No need to probe because of interaction between a=4MGN|1|A|A|83 B=4MGN|1|A|U|21
pMakeNodes making a cluster near strand break a=4MGN|1|A|A|83 B=4MGN|1|A|U|21
pMakeNodesCluster: amax is 11 bmin is 12, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 3 and then 18 to 19
aa is 3 bb is 18
  4 Cluster   4MGN|1|A|A|83:4MGN|1|A|A|83 4MGN|1|A|G|20:4MGN|1|A|U|21
    LR Inter  4MGN|1|A|A|83 4MGN|1|A|U|21 tHW 
    RR Inter  4MGN|1|A|G|20 4MGN|1|A|U|21 cSH 
pMakeNodesCluster a=4 B=17 at the end
pMakeNodesCluster a=4 B=17 at the end
No need to probe because of interaction between a=4MGN|1|A|A|84 B=4MGN|1|A|A|19
  5 Basepair    84   19 AA tHH 
pMakeNodes probe for inserts:  a=4MGN|1|A|A|85 B=4MGN|1|A|U|18
    Insertion on left  4MGN|1|A|A|85
    Insertion on left  4MGN|1|A|C|86
    Insertion on left  4MGN|1|A|G|87
    Insertion on left  4MGN|1|A|G|88
    Insertion on left  4MGN|1|A|C|89
    Insertion on right 4MGN|1|A|U|18
    Insertion on right 4MGN|1|A|A|17
    Insertion on right 4MGN|1|A|A|16
pMakeNodesProbeForInsertions:  a 4MGN|1|A|A|90 interacts with 4MGN|1|A|C|15
pMakeNodesProbeForInsertions:  B 4MGN|1|A|C|15 interacts with 4MGN|1|A|A|90
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4MGN|1|A|C|15 interacts with 4MGN|1|A|A|90
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4MGN|1|A|A|90 B=4MGN|1|A|C|15
  6 Basepair    90   15 AC bif 
No need to probe because of interaction between a=4MGN|1|A|G|91 B=4MGN|1|A|U|14
  7 Basepair    91   14 GU cWW 
  8 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 21
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 21
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 20
pMakeMotifModelFromSSF:   4   Cluster Left  3 Right 18 19
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right 17
pMakeMotifModelFromSSF:   6  Basepair Left 10 Right 13
pMakeMotifModelFromSSF:   7  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:   8   Hairpin Left 12 Right 11
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4MGN|1|A|U|18
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4MGN|1|A|A|19
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4MGN|1|A|G|20
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4MGN|1|A|U|21
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4MGN|1|A|A|22
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4MGN|1|A|C|86
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4MGN|1|A|A|85
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4MGN|1|A|A|84
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 21
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [21×21 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 21
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U81 - G23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 20
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G82 - A22 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: 3
            RightIndex: [18 19]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'A'
           RightLetter: 'GU'
               Comment: ' // Cluster node 4MGN|1|A|A|83:4MGN|1|A|A|83 and 4MGN|1|A|G|20:4MGN|1|A|U|21'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: 1
                 Right: [1 2]
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2971

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 17
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-06 8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AACGGC'
           RightLetter: 'AAUA'
               Comment: ' // Basepair A84 - A19 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4MGN|1|A|U|18'
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4MGN|1|A|A|19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
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                IBases: [1 1]
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          InterIndices: []
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                  rpar: []
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Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 16
             Insertion: []
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
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            RightIndex: 16
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       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4MGN|1|A|G|20'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 8
            RightIndex: 16
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       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 14
             LeftIndex: 8
            RightIndex: 16
             Insertion: []
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        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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               Comment: ' // Fixed node on left for 4MGN|1|A|U|21'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
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Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 15
             LeftIndex: 9
            RightIndex: 16
             Insertion: []
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        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 16
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            RightIndex: 16
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        leftLengthDist: [0 1]
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       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
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           RightLetter: ''
               Comment: ' // Fixed node on left for 4MGN|1|A|A|22'
              NumLoops: []
                  Edge: []
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                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
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Node 16

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 17
             LeftIndex: 10
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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Node 17

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 18
             LeftIndex: 10
            RightIndex: 16
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4MGN|1|A|C|86'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 18

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 19
             LeftIndex: 10
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 19

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 20
             LeftIndex: 10
            RightIndex: 15
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4MGN|1|A|A|85'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
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Node 20

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 21
             LeftIndex: 10
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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                  rpar: []
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Node 21

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 22
             LeftIndex: 10
            RightIndex: 14
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4MGN|1|A|A|84'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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                  rpar: []
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Node 22

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 23
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
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      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
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Node 23

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 24
             LeftIndex: 10
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A90 - C15 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
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Node 24

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 25
             LeftIndex: 11
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G91 - U14 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
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          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
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Node 25

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 27
             LeftIndex: 12
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 12
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 21
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 21
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 20
pMakeMotifModelFromSSF:   4   Cluster Left  3 Right 18 19
pMakeMotifModelFromSSF:   5   Initial Left  4 Right 17
pMakeMotifModelFromSSF:   6  Basepair Left  4 Right 17
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right 16
pMakeMotifModelFromSSF:   8   Initial Left  6 Right 16
pMakeMotifModelFromSSF:   9     Fixed Left  6 Right 16
pMakeMotifModelFromSSF:  10   Initial Left  7 Right 16
pMakeMotifModelFromSSF:  11     Fixed Left  7 Right 16
pMakeMotifModelFromSSF:  12   Initial Left  8 Right 16
pMakeMotifModelFromSSF:  13     Fixed Left  8 Right 16
pMakeMotifModelFromSSF:  14   Initial Left  9 Right 16
pMakeMotifModelFromSSF:  15     Fixed Left  9 Right 16
pMakeMotifModelFromSSF:  16   Initial Left 10 Right 16
pMakeMotifModelFromSSF:  17     Fixed Left 10 Right 16
pMakeMotifModelFromSSF:  18   Initial Left 10 Right 15
pMakeMotifModelFromSSF:  19     Fixed Left 10 Right 15
pMakeMotifModelFromSSF:  20   Initial Left 10 Right 14
pMakeMotifModelFromSSF:  21     Fixed Left 10 Right 14
pMakeMotifModelFromSSF:  22   Initial Left 10 Right 13
pMakeMotifModelFromSSF:  23  Basepair Left 10 Right 13
pMakeMotifModelFromSSF:  24  Basepair Left 11 Right 12
pMakeMotifModelFromSSF:  25   Hairpin Left 12 Right 11
pNextNodeJunction: Found a hairpin at node 25
pNextNodeJunction: Found a hairpin at node 25

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_93889.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

  -11.3153

Timestamp 18-Jul-2025 22:49:02
pMakeSCFGModels: Making JAR3D model for motif group IL_94351.1, number 389 of 411
pMakeNodes starting loop:     a=1OOA|1|C|C|5 B=1OOA|1|C|G|25
  2 Basepair     5   25 CG cWW 
No need to probe because of interaction between a=1OOA|1|C|U|6 B=1OOA|1|C|C|24
  3 Basepair     6   24 UC tSH 
pMakeNodes probe for inserts:  a=1OOA|1|C|U|7 B=1OOA|1|C|G|23
    Insertion on left  1OOA|1|C|U|7
    Insertion on left  1OOA|1|C|G|8
    Insertion on right 1OOA|1|C|G|23
pMakeNodesProbeForInsertions:  a 1OOA|1|C|A|9 interacts with 1OOA|1|C|G|22
pMakeNodesProbeForInsertions:  B 1OOA|1|C|G|22 interacts with 1OOA|1|C|A|9
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 1OOA|1|C|G|22 interacts with 1OOA|1|C|A|9
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=1OOA|1|C|A|9 B=1OOA|1|C|G|22
  4 Basepair     9   22 AG tHS 
No need to probe because of interaction between a=1OOA|1|C|A|10 B=1OOA|1|C|U|21
  5 Basepair    10   21 AU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1OOA|1|C|U|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1OOA|1|C|G|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 1OOA|1|C|G|23
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
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                IBases: []
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          InterIndices: []
                  lpar: []
                  rpar: []
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Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C5 - G25 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UUG'
           RightLetter: 'GC'
               Comment: ' // Basepair U6 - C24 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1OOA|1|C|U|7'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1OOA|1|C|G|8'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 1OOA|1|C|G|23'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A9 - G22 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A10 - U21 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  9
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  9
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  9
pMakeMotifModelFromSSF:   7   Initial Left  5 Right  9
pMakeMotifModelFromSSF:   8     Fixed Left  5 Right  9
pMakeMotifModelFromSSF:   9   Initial Left  5 Right  8
pMakeMotifModelFromSSF:  10  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  12   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_94351.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.4815

Timestamp 18-Jul-2025 22:49:02
pMakeSCFGModels: Making JAR3D model for motif group IL_94684.1, number 390 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|U|1393 B=8CRE|1|CM|A|1377
  2 Basepair  1393 1377 UA cWW 
pMakeNodes probe for inserts:  a=8CRE|1|CM|G|1394 B=8CRE|1|CM|U|1376
    Insertion on right 8CRE|1|CM|U|1376
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|G|1394 interacts with 8CRE|1|CM|G|1398
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|C|1375 interacts with 8CRE|1|CM|G|1398
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|C|1375 interacts with 8CRE|1|CM|G|1398
pMakeNodes probed for insert:  a=8CRE|1|CM|G|1394 B=8CRE|1|CM|C|1375
pMakeNodes making a cluster near strand break a=8CRE|1|CM|G|1394 B=8CRE|1|CM|C|1375
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 6 and then 7 to 7
aa is 6 bb is 7
  3 Cluster   8CRE|1|CM|G|1394:8CRE|1|CM|G|1398 8CRE|1|CM|C|1375:8CRE|1|CM|C|1375
    LR Inter  8CRE|1|CM|G|1398 8CRE|1|CM|C|1375 cWW 
    LL Inter  8CRE|1|CM|G|1394 8CRE|1|CM|G|1398 tWH 
    Left  strand conserved insertion 8CRE|1|CM|G|1395 at position 2
    Left  strand conserved insertion 8CRE|1|CM|A|1396 at position 3
    Left  strand conserved insertion 8CRE|1|CM|A|1397 at position 4
pMakeNodesCluster a=7 B=6 at the end
pMakeNodesCluster a=7 B=6 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 8CRE|1|CM|A|1397
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'UA'
               Comment: ' // Basepair U1393 - A1377 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 8CRE|1|CM|A|1397'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 0.2516

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 6
             LeftIndex: [2 3 4 5 6]
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGAAG'
           RightLetter: 'C'
               Comment: ' // Cluster node 8CRE|1|CM|G|1394:8CRE|1|CM|G|1398 and 8CRE|1|CM|C|1375:8CRE|1|CM|C|1375'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 0.2516

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  2 Right  7
pMakeMotifModelFromSSF:   5   Cluster Left  2  3  4  5  6 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  7 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 7
pUpdateModelWithSSF: IL_94684.1 allow insertions from initial node 6?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_94684.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.6421
   -3.6421

Timestamp 18-Jul-2025 22:49:02
pMakeSCFGModels: Making JAR3D model for motif group IL_94910.1, number 391 of 411
pMakeNodes starting loop:     a=7A0S|1|X|C|96 B=7A0S|1|X|G|84
pMakeNodes making a cluster near strand break a=7A0S|1|X|C|96 B=7A0S|1|X|G|84
pMakeNodesCluster: amax is 7 bmin is 8, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 10 to 12
aa is 5 bb is 10
  2 Cluster   7A0S|1|X|C|96:7A0S|1|X|A|101 7A0S|1|X|G|82:7A0S|1|X|G|84
    LR Inter  7A0S|1|X|A|101 7A0S|1|X|G|82 tHS 
    LR Inter  7A0S|1|X|U|97 7A0S|1|X|A|83 tSS 
    LR Inter  7A0S|1|X|G|100 7A0S|1|X|A|83 tSH 
    LR Inter  7A0S|1|X|C|96 7A0S|1|X|G|84 cWW 
    LR Inter  7A0S|1|X|A|101 7A0S|1|X|G|84 tSS 
    Left  strand conserved insertion 7A0S|1|X|U|98 at position 3
pMakeNodesCluster a=6 B=9 at the end
pMakeNodesCluster a=6 B=9 at the end
No need to probe because of interaction between a=7A0S|1|X|C|102 B=7A0S|1|X|C|81
  3 Basepair   102   81 CC bif 
No need to probe because of interaction between a=7A0S|1|X|U|103 B=7A0S|1|X|A|80
  4 Basepair   103   80 UA cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 10 11 12
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 12
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [12×12 double]
         Extensibility: [0 0 0 0 0 0 1 1 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: [10 11 12]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CUUGA'
           RightLetter: 'GAG'
               Comment: ' // Cluster node 7A0S|1|X|C|96:7A0S|1|X|A|101 and 7A0S|1|X|G|82:7A0S|1|X|G|84'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
          LeftNotInter: 3
         RightNotInter: [1×0 double]
              NormCons: 0.0247
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C102 - C81 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U103 - A80 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 12
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 10 11 12
pMakeMotifModelFromSSF:   3   Initial Left  6 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   6   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_94910.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.3526
   -7.1563
   -7.2197

Timestamp 18-Jul-2025 22:49:03
pMakeSCFGModels: Making JAR3D model for motif group IL_94967.1, number 392 of 411
pMakeNodes starting loop:     a=6JOO|1|B|G|61 B=6JOO|1|B|C|58
  2 Basepair    61   58 GC cWW 
pMakeNodes probe for inserts:  a=6JOO|1|B|U|62 B=6JOO|1|B|G|57
    Insertion on left  6JOO|1|B|U|62
    Insertion on left  6JOO|1|B|U|64
pMakeNodesProbeForInsertions:  a 6JOO|1|B|C|65 interacts with 6JOO|1|B|G|57
pMakeNodesProbeForInsertions:  B 6JOO|1|B|G|57 interacts with 6JOO|1|B|C|65
pMakeNodesProbeForInsertions:  B 6JOO|1|B|G|57 interacts with 6JOO|1|B|C|65
pMakeNodes probed for insert:  a=6JOO|1|B|C|65 B=6JOO|1|B|G|57
  3 Basepair    65   57 CG cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6JOO|1|B|C|58
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6JOO|1|B|G|61
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GUU'
           RightLetter: 'C'
               Comment: ' // Basepair G61 - C58 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6JOO|1|B|C|58'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6JOO|1|B|G|61'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C65 - G57 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  5
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  5
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  5
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   7  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   8   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_94967.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.2378

Timestamp 18-Jul-2025 22:49:03
pMakeSCFGModels: Making JAR3D model for motif group IL_95570.1, number 393 of 411
pMakeNodes starting loop:     a=6CK5|1|A|U|36 B=6CK5|1|A|G|23
  2 Basepair    36   23 UG cWW 
pMakeNodes probe for inserts:  a=6CK5|1|A|G|37 B=6CK5|1|A|A|22
pMakeNodesProbeForInsertions:  a 6CK5|1|A|G|37 interacts with 6CK5|1|A|G|41
pMakeNodesProbeForInsertions:  B 6CK5|1|A|A|22 interacts with 6CK5|1|A|U|39
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but B makes a more important one
pMakeNodesProbeForInsertions:  B 6CK5|1|A|A|22 interacts with 6CK5|1|A|U|39
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=6CK5|1|A|G|37 B=6CK5|1|A|A|22
pMakeNodes making a cluster near strand break a=6CK5|1|A|G|37 B=6CK5|1|A|A|22
pMakeNodesCluster: amax is 4 bmin is 5, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 4 and then 5 to 6
aa is 4 bb is 5
  3 Cluster   6CK5|1|A|G|37:6CK5|1|A|G|41 6CK5|1|A|C|21:6CK5|1|A|A|22
    LR Inter  6CK5|1|A|G|41 6CK5|1|A|C|21 cWW 
    LR Inter  6CK5|1|A|U|39 6CK5|1|A|A|22 cWW 
    LL Inter  6CK5|1|A|G|37 6CK5|1|A|G|41 cWH 
pMakeNodesCluster a=5 B=4 at the end
pMakeNodesCluster a=5 B=4 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  5  6
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U36 - G23 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4]
            RightIndex: [5 6]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GUG'
           RightLetter: 'CA'
               Comment: ' // Cluster node 6CK5|1|A|G|37:6CK5|1|A|G|41 and 6CK5|1|A|C|21:6CK5|1|A|A|22'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: [1 2]
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2515

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4 Right  5  6
pMakeMotifModelFromSSF:   4   Initial Left  5 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_95570.1 allow insertions from initial node 4?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_95570.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.3313
   -6.5032

Timestamp 18-Jul-2025 22:49:03
pMakeSCFGModels: Making JAR3D model for motif group IL_95583.2, number 394 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|1837 B=5J7L|1|DA|G|1903
pMakeNodes making a cluster near strand break a=5J7L|1|DA|C|1837 B=5J7L|1|DA|G|1903
pMakeNodesCluster: amax is 3 bmin is 4, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 5 to 5
aa is 2 bb is 5
  2 Cluster   5J7L|1|DA|C|1837:5J7L|1|DA|G|1839 5J7L|1|DA|G|1903:5J7L|1|DA|G|1903
    LR Inter  5J7L|1|DA|C|1837 5J7L|1|DA|G|1903 cWW 
    LR Inter  5J7L|1|DA|G|1839 5J7L|1|DA|G|1903 tHS 
pMakeNodesCluster a=3 B=4 at the end
pMakeNodesCluster a=3 B=4 at the end
No need to probe because of interaction between a=5J7L|1|DA|G|1840 B=5J7L|1|DA|C|1902
  3 Basepair  1840 1902 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  5
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   4   Hairpin Left  4 Right  3
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 5
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [5×5 double]
         Extensibility: [0 0 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CG'
           RightLetter: 'G'
               Comment: ' // Cluster node 5J7L|1|DA|C|1837:5J7L|1|DA|G|1839 and 5J7L|1|DA|G|1903:5J7L|1|DA|G|1903'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2505
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G1840 - C1902 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  5
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right  5
pMakeMotifModelFromSSF:   3   Initial Left  3 Right  4
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_95583.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -3.8424
   -3.8424
   -4.4400
   -4.6004
   -4.6004
   -4.6004
   -3.8424
   -5.8709
   -7.0053
   -8.1154
   -5.8176

Timestamp 18-Jul-2025 22:49:03
pMakeSCFGModels: Making JAR3D model for motif group IL_95727.1, number 395 of 411
pMakeNodes starting loop:     a=4LFB|1|A|C|699 B=4LFB|1|A|G|688
pMakeNodes making a cluster near strand break a=4LFB|1|A|C|699 B=4LFB|1|A|G|688
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 12 to 14
aa is 5 bb is 12
  2 Cluster   4LFB|1|A|C|699:4LFB|1|A|A|704 4LFB|1|A|U|686:4LFB|1|A|G|688
    LR Inter  4LFB|1|A|A|704 4LFB|1|A|U|686 tHW 
    LR Inter  4LFB|1|A|G|703 4LFB|1|A|A|687 tSH 
    LR Inter  4LFB|1|A|C|699 4LFB|1|A|G|688 cWW 
    LR Inter  4LFB|1|A|A|704 4LFB|1|A|G|688 tSS 
    Left  strand conserved insertion 4LFB|1|A|G|700 at position 2
    Left  strand conserved insertion 4LFB|1|A|C|701 at position 3
pMakeNodesCluster a=6 B=11 at the end
pMakeNodesCluster a=6 B=11 at the end
No need to probe because of interaction between a=4LFB|1|A|U|705 B=4LFB|1|A|G|685
  3 Basepair   705  685 UG tHS 
pMakeNodes probe for inserts:  a=4LFB|1|A|A|706 B=4LFB|1|A|A|684
    Insertion on left  4LFB|1|A|A|706
    Insertion on right 4LFB|1|A|A|684
pMakeNodesProbeForInsertions:  a 4LFB|1|A|C|707 interacts with 4LFB|1|A|G|683
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|683 interacts with 4LFB|1|A|C|707
pMakeNodesProbeForInsertions:  B 4LFB|1|A|G|683 interacts with 4LFB|1|A|C|707
pMakeNodes probed for insert:  a=4LFB|1|A|C|707 B=4LFB|1|A|G|683
  4 Basepair   707  683 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 12 13 14
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4LFB|1|A|C|699
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4LFB|1|A|A|702
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 14
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [14×14 double]
         Extensibility: [0 0 0 0 0 0 1 1 1 1 0 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: [12 13 14]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CGCGA'
           RightLetter: 'UAG'
               Comment: ' // Cluster node 4LFB|1|A|C|699:4LFB|1|A|A|704 and 4LFB|1|A|U|686:4LFB|1|A|G|688'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.1008
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UA'
           RightLetter: 'AG'
               Comment: ' // Basepair U705 - G685 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4LFB|1|A|C|699'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 8
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4LFB|1|A|A|702'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C707 - G683 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 14
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 12 13 14
pMakeMotifModelFromSSF:   3   Initial Left  6 Right 11
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right 11
pMakeMotifModelFromSSF:   5     Fixed Left  7 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  8 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  8 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  8 Right  9
pMakeMotifModelFromSSF:   9  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  10   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_95727.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.5018

Timestamp 18-Jul-2025 22:49:03
pMakeSCFGModels: Making JAR3D model for motif group IL_95811.1, number 396 of 411
pMakeNodes starting loop:     a=1ET4|1|A|C|211 B=1ET4|1|A|G|230
  2 Basepair   211  230 CG cWW 
pMakeNodes probe for inserts:  a=1ET4|1|A|G|212 B=1ET4|1|A|C|229
    Insertion on left  1ET4|1|A|G|212
    Insertion on left  1ET4|1|A|C|213
    Insertion on left  1ET4|1|A|A|214
pMakeNodesProbeForInsertions:  a 1ET4|1|A|U|215 interacts with 1ET4|1|A|C|229
pMakeNodesProbeForInsertions:  B 1ET4|1|A|C|229 interacts with 1ET4|1|A|U|215
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 1ET4|1|A|C|229 interacts with 1ET4|1|A|A|217
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=1ET4|1|A|U|215 B=1ET4|1|A|C|229
pMakeNodes making a cluster near strand break a=1ET4|1|A|U|215 B=1ET4|1|A|C|229
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 5 to 7 and then 10 to 10
aa is 7 bb is 10
  3 Cluster   1ET4|1|A|U|215:1ET4|1|A|A|217 1ET4|1|A|C|229:1ET4|1|A|C|229
    LR Inter  1ET4|1|A|U|215 1ET4|1|A|C|229 cWW 
    LR Inter  1ET4|1|A|A|217 1ET4|1|A|C|229 bif 
    Left  strand conserved insertion 1ET4|1|A|A|216 at position 2
pMakeNodesCluster a=8 B=9 at the end
pMakeNodesCluster a=8 B=9 at the end
No need to probe because of interaction between a=1ET4|1|A|C|218 B=1ET4|1|A|G|228
  4 Basepair   218  228 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3   Cluster Left  5  6  7 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   5   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1ET4|1|A|G|212
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1ET4|1|A|C|213
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 1ET4|1|A|A|214
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1900e-04 0.0082 0.0819 0.8190 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGCA'
           RightLetter: 'G'
               Comment: ' // Basepair C211 - G230 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1ET4|1|A|G|212'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.3762

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1ET4|1|A|C|213'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 1ET4|1|A|A|214'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 10
             LeftIndex: [5 6 7]
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UAA'
           RightLetter: 'C'
               Comment: ' // Cluster node 1ET4|1|A|U|215:1ET4|1|A|A|217 and 1ET4|1|A|C|229:1ET4|1|A|C|229'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×3 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3]
                 Right: 1
      InsertionComment: []
                IBases: [3×2 double]
    InteractionComment: {1×3 cell}
      JunctionDeletion: []
          InterIndices: [3×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: 2
         RightNotInter: [1×0 double]
              NormCons: 0.3762

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C218 - G228 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9   Cluster Left  5  6  7 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  8 Right  9
pMakeMotifModelFromSSF:  11  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:  12   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_95811.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.7537

Timestamp 18-Jul-2025 22:49:04
pMakeSCFGModels: Making JAR3D model for motif group IL_96236.1, number 397 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|A|844 B=5J7L|1|DA|U|934
  2 Basepair   844  934 AU cWW 
pMakeNodes probe for inserts:  a=5J7L|1|DA|A|845||A B=5J7L|1|DA|A|933
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|A|845||A interacts with 5J7L|1|DA|U|932
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|933 interacts with 5J7L|1|DA|U|847||A
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|A|933 interacts with 5J7L|1|DA|U|847||A
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5J7L|1|DA|A|845||A B=5J7L|1|DA|A|933
pMakeNodes making a cluster near strand break a=5J7L|1|DA|A|845||A B=5J7L|1|DA|A|933
pMakeNodesCluster: amax is 5 bmin is 6, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 5 and then 6 to 8
aa is 5 bb is 6
  3 Cluster   5J7L|1|DA|A|845||A:5J7L|1|DA|C|848 5J7L|1|DA|G|930:5J7L|1|DA|A|933
    LR Inter  5J7L|1|DA|C|848 5J7L|1|DA|G|930 cWW 
    LR Inter  5J7L|1|DA|A|845||A 5J7L|1|DA|U|932 tWW 
    LR Inter  5J7L|1|DA|U|847||A 5J7L|1|DA|A|933 cWW 
    LL Inter  5J7L|1|DA|U|846||A 5J7L|1|DA|C|848 cSH 
pMakeNodesCluster a=6 B=5 at the end
pMakeNodesCluster a=6 B=5 at the end
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5 Right  6  7  8
pMakeMotifModelFromSSF:   4   Hairpin Left  6 Right  5
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9950 0.0045 5.0000e-04]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A844 - U934 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5]
            RightIndex: [6 7 8]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'AUUC'
           RightLetter: 'GUA'
               Comment: ' // Cluster node 5J7L|1|DA|A|845||A:5J7L|1|DA|C|848 and 5J7L|1|DA|G|930:5J7L|1|DA|A|933'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2510

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5 Right  6  7  8
pMakeMotifModelFromSSF:   4   Initial Left  6 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 5
pUpdateModelWithSSF: IL_96236.1 allow insertions from initial node 4?
ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0


ans =

    0.9524    0.0476


ans =

    0.2500    0.2500    0.2500    0.2500         0

pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_96236.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -5.4083

Timestamp 18-Jul-2025 22:49:04
pMakeSCFGModels: Making JAR3D model for motif group IL_96303.1, number 398 of 411
pMakeNodes starting loop:     a=8HBA|1|B|G|6 B=8HBA|1|B|C|32
pMakeNodes making a cluster near strand break a=8HBA|1|B|G|6 B=8HBA|1|B|C|32
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 2 and then 13 to 13
aa is 2 bb is 13
  2 Cluster   8HBA|1|B|G|6:8HBA|1|B|U|7 8HBA|1|B|C|32:8HBA|1|B|C|32
    LR Inter  8HBA|1|B|G|6 8HBA|1|B|C|32 cWW 
    LL Inter  8HBA|1|B|G|6 8HBA|1|B|U|7 cSH 
pMakeNodesCluster a=3 B=12 at the end
pMakeNodesCluster a=3 B=12 at the end
pMakeNodes probe for inserts:  a=8HBA|1|B|U|8 B=8HBA|1|B|A|31
pMakeNodesProbeForInsertions:  a 8HBA|1|B|U|8 interacts with 8HBA|1|B|G|15
pMakeNodesProbeForInsertions:  B 8HBA|1|B|A|31 interacts with 8HBA|1|B|G|15
pMakeNodesProbeForInsertions:  Both a and B make nested interactions, but a makes a more important one
pMakeNodesProbeForInsertions:  B 8HBA|1|B|A|31 interacts with 8HBA|1|B|G|15
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  3 Initial      8 (0 insertion) and   31 (0 insertion)
pMakeNodes probed for insert:  a=8HBA|1|B|U|8 B=8HBA|1|B|A|31
pMakeNodes making a cluster near strand break a=8HBA|1|B|U|8 B=8HBA|1|B|A|31
pMakeNodesCluster: amax is 10 bmin is 11, use_amax is 1
pMakeNodesCluster: Cluster goes from 3 to 7 and then 12 to 12
aa is 7 bb is 12
  4 Cluster   8HBA|1|B|U|8:8HBA|1|B|G|15 8HBA|1|B|A|31:8HBA|1|B|A|31
    LR Inter  8HBA|1|B|G|15 8HBA|1|B|A|31 tSW 
    LL Inter  8HBA|1|B|U|8 8HBA|1|B|G|15 tHW 
    Left  strand conserved insertion 8HBA|1|B|U|12 at position 2
    Left  strand conserved insertion 8HBA|1|B|C|13 at position 3
    Left  strand conserved insertion 8HBA|1|B|C|14 at position 4
pMakeNodesCluster a=8 B=11 at the end
pMakeNodesCluster a=8 B=11 at the end
pMakeNodes probe for inserts:  a=8HBA|1|B|A|17 B=8HBA|1|B|C|30
    Insertion on left  8HBA|1|B|A|17
    Insertion on left  8HBA|1|B|A|18
pMakeNodesProbeForInsertions:  a 8HBA|1|B|G|19 interacts with 8HBA|1|B|C|30
pMakeNodesProbeForInsertions:  B 8HBA|1|B|C|30 interacts with 8HBA|1|B|G|19
pMakeNodesProbeForInsertions:  B 8HBA|1|B|C|30 interacts with 8HBA|1|B|G|19
  5 Initial     17 (2 insertion) and   30 (0 insertion)
pMakeNodes probed for insert:  a=8HBA|1|B|G|19 B=8HBA|1|B|C|30
  6 Basepair    19   30 GC cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 13
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6  7 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  8 Right 11
pMakeMotifModelFromSSF:   6  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:   7   Hairpin Left 11 Right 10
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8HBA|1|B|C|13
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8HBA|1|B|C|14
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 0 1 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2]
            RightIndex: 13
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GU'
           RightLetter: 'C'
               Comment: ' // Cluster node 8HBA|1|B|G|6:8HBA|1|B|U|7 and 8HBA|1|B|C|32:8HBA|1|B|C|32'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×2 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2]
                 Right: 1
      InsertionComment: []
                IBases: [2×2 double]
    InteractionComment: {1×2 cell}
      JunctionDeletion: []
          InterIndices: [2×2 double]
          LeftNotInter: [1×0 double]
         RightNotInter: [1×0 double]
              NormCons: 0.2501
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 3
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: []
           RightLetter: []
               Comment: ' // Initial node 8HBA|1|B|U|8 - 8HBA|1|B|A|31 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 5
             LeftIndex: [3 4 5 6 7]
            RightIndex: 12
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'UUCCG'
           RightLetter: 'A'
               Comment: ' // Cluster node 8HBA|1|B|U|8:8HBA|1|B|G|15 and 8HBA|1|B|A|31:8HBA|1|B|A|31'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×5 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: 1
      InsertionComment: []
                IBases: [5×2 double]
    InteractionComment: {1×5 cell}
      JunctionDeletion: []
          InterIndices: [5×2 double]
          LeftNotInter: [2 3 4]
         RightNotInter: [1×0 double]
              NormCons: 0.2689
                  lpar: []
                  rpar: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AA'
           RightLetter: []
               Comment: ' // Initial node 8HBA|1|B|A|17 - 8HBA|1|B|C|30 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 8
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8HBA|1|B|C|13'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 9
             LeftIndex: 9
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8HBA|1|B|C|14'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 10
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 11
             LeftIndex: 10
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G19 - C30 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 11
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 11
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2   Cluster Left  1  2 Right 13
pMakeMotifModelFromSSF:   3   Initial Left  3 Right 12
pMakeMotifModelFromSSF:   4   Cluster Left  3  4  5  6  7 Right 12
pMakeMotifModelFromSSF:   5   Initial Left  8 Right 11
pMakeMotifModelFromSSF:   6     Fixed Left  8 Right 11
pMakeMotifModelFromSSF:   7   Initial Left  9 Right 11
pMakeMotifModelFromSSF:   8     Fixed Left  9 Right 11
pMakeMotifModelFromSSF:   9   Initial Left 10 Right 11
pMakeMotifModelFromSSF:  10  Basepair Left 10 Right 11
pMakeMotifModelFromSSF:  11   Hairpin Left 11 Right 10
pNextNodeJunction: Found a hairpin at node 11
pNextNodeJunction: Found a hairpin at node 11

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_96303.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -9.3544
   -9.3544
  -10.6537

Timestamp 18-Jul-2025 22:49:04
pMakeSCFGModels: Making JAR3D model for motif group IL_96332.5, number 399 of 411
pMakeNodes starting loop:     a=8K85|1|A|G|4 B=8K85|1|B|C|53
  2 Basepair     4   53 GC cWW 
No need to probe because of interaction between a=8K85|1|A|A|5 B=8K85|1|B|G|52
  3 Basepair     5   52 AG cWW 
No need to probe because of interaction between a=8K85|1|A|C|6 B=8K85|1|B|G|51
  4 Basepair     6   51 CG cWW 
pMakeNodes probe for inserts:  a=8K85|1|A|G|7 B=8K85|1|B|G|50
    Insertion on left  8K85|1|A|G|7
    Insertion on left  8K85|1|A|G|8
pMakeNodesProbeForInsertions:  a 8K85|1|A|C|10 interacts with 8K85|1|B|G|50
pMakeNodesProbeForInsertions:  B 8K85|1|B|G|50 interacts with 8K85|1|A|C|10
pMakeNodesProbeForInsertions:  B 8K85|1|B|G|50 interacts with 8K85|1|A|C|10
pMakeNodes probed for insert:  a=8K85|1|A|C|10 B=8K85|1|B|G|50
  5 Basepair    10   50 CG cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8K85|1|A|G|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8K85|1|A|G|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G4 - C53 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A5 - G52 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'CGG'
           RightLetter: 'G'
               Comment: ' // Basepair C6 - G51 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8K85|1|A|G|7'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8K85|1|A|G|8'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C10 - G50 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   7     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   9  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  10   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_96332.5_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8222
   -6.8222
   -6.8222
   -6.9497
   -6.9497
   -8.4295
  -13.4630

Timestamp 18-Jul-2025 22:49:04
pMakeSCFGModels: Making JAR3D model for motif group IL_96371.1, number 400 of 411
pMakeNodes starting loop:     a=6CK5|1|A|U|80 B=6CK5|1|A|G|97
  2 Basepair    80   97 UG cWW 
No need to probe because of interaction between a=6CK5|1|A|A|81 B=6CK5|1|A|G|95
  3 Basepair    81   95 AG tHH 
No need to probe because of interaction between a=6CK5|1|A|G|82 B=6CK5|1|A|C|94
  4 Basepair    82   94 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [6×6 double]
         Extensibility: [0 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'G'
               Comment: ' // Basepair U80 - G97 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A81 - G95 tHH '
              NumLoops: []
                  Edge: 8
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G82 - C94 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 3
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 4
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  6
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  6
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  5
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  4
pMakeMotifModelFromSSF:   5   Hairpin Left  4 Right  3
pNextNodeJunction: Found a hairpin at node 5
pNextNodeJunction: Found a hairpin at node 5

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_96371.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.2663

Timestamp 18-Jul-2025 22:49:05
pMakeSCFGModels: Making JAR3D model for motif group IL_96759.1, number 401 of 411
pMakeNodes starting loop:     a=5V1K|1|B|C|203 B=5V1K|1|A|G|110
  2 Basepair   203  110 CG cWW 
No need to probe because of interaction between a=5V1K|1|B|G|204 B=5V1K|1|A|A|109
  3 Basepair   204  109 GA tSH 
pMakeNodes probe for inserts:  a=5V1K|1|B|A|205 B=5V1K|1|A|8RJ|108||A
    Insertion on left  5V1K|1|B|A|205
    Insertion on right 5V1K|1|A|8RJ|108||A
pMakeNodesProbeForInsertions:  a 5V1K|1|B|A|206 interacts with 5V1K|1|A|5BU|107||A
pMakeNodesProbeForInsertions:  B 5V1K|1|A|5BU|107||A interacts with 5V1K|1|B|A|206
pMakeNodesProbeForInsertions:  B 5V1K|1|A|5BU|107||A interacts with 5V1K|1|B|A|206
pMakeNodes probed for insert:  a=5V1K|1|B|A|206 B=5V1K|1|A|5BU|107||A
  4 Basepair   206  107 AU cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5V1K|1|B|A|205
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5V1K|1|A|8RJ|108||A
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C203 - G110 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'UA'
               Comment: ' // Basepair G204 - A109 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5V1K|1|B|A|205'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5V1K|1|A|8RJ|108||A'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A206 - U107 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   5   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   6     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   7   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_96759.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.8877

Timestamp 18-Jul-2025 22:49:05
pMakeSCFGModels: Making JAR3D model for motif group IL_96788.1, number 402 of 411
pMakeNodes starting loop:     a=3IGI|1|A|G|267 B=3IGI|1|A|C|286
  2 Basepair   267  286 GC cWW 
No need to probe because of interaction between a=3IGI|1|A|A|268 B=3IGI|1|A|U|285
  3 Basepair   268  285 AU tHW 
No need to probe because of interaction between a=3IGI|1|A|G|269 B=3IGI|1|A|G|284
  4 Basepair   269  284 GG tHS 
No need to probe because of interaction between a=3IGI|1|A|G|270 B=3IGI|1|A|A|283
  5 Basepair   270  283 GA cWW 
No need to probe because of interaction between a=3IGI|1|A|U|271 B=3IGI|1|A|A|282
  6 Basepair   271  282 UA cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [10×10 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G267 - C286 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A268 - U285 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'G'
               Comment: ' // Basepair G269 - G284 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'A'
               Comment: ' // Basepair G270 - A283 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U271 - A282 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 8
             LeftIndex: 6
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 6
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 10
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 10
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  8
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  7
pMakeMotifModelFromSSF:   6  Basepair Left  5 Right  6
pMakeMotifModelFromSSF:   7   Hairpin Left  6 Right  5
pNextNodeJunction: Found a hairpin at node 7
pNextNodeJunction: Found a hairpin at node 7

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_96788.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.3375

Timestamp 18-Jul-2025 22:49:05
pMakeSCFGModels: Making JAR3D model for motif group IL_97273.1, number 403 of 411
pMakeNodes starting loop:     a=8P9A|1|sR|G|985 B=8P9A|1|sR|C|1016
  2 Basepair   985 1016 GC cWW 
No need to probe because of interaction between a=8P9A|1|sR|G|986 B=8P9A|1|sR|U|1015
pMakeNodes making a cluster near strand break a=8P9A|1|sR|G|986 B=8P9A|1|sR|U|1015
pMakeNodesCluster: amax is 6 bmin is 7, use_amax is 1
pMakeNodesCluster: Cluster goes from 2 to 5 and then 8 to 8
aa is 5 bb is 8
  3 Cluster   8P9A|1|sR|G|986:8P9A|1|sR|U|989 8P9A|1|sR|U|1015:8P9A|1|sR|U|1015
    LR Inter  8P9A|1|sR|G|986 8P9A|1|sR|U|1015 tSH 
    LR Inter  8P9A|1|sR|U|989 8P9A|1|sR|U|1015 cWW 
    Left  strand conserved insertion 8P9A|1|sR|G|987 at position 2
    Left  strand conserved insertion 8P9A|1|sR|A|988 at position 3
pMakeNodesCluster a=6 B=7 at the end
pMakeNodesCluster a=6 B=7 at the end
No need to probe because of interaction between a=8P9A|1|sR|C|990 B=8P9A|1|sR|G|1014
  4 Basepair   990 1014 CG cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5 Right  8
pMakeMotifModelFromSSF:   4  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   5   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after Cluster
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [9×9 double]
         Extensibility: [0 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G985 - C1016 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 4
             LeftIndex: [2 3 4 5]
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'GGAU'
           RightLetter: 'U'
               Comment: ' // Cluster node 8P9A|1|sR|G|986:8P9A|1|sR|U|989 and 8P9A|1|sR|U|1015:8P9A|1|sR|U|1015'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×4 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4]
                 Right: 1
      InsertionComment: []
                IBases: [4×2 double]
    InteractionComment: {1×4 cell}
      JunctionDeletion: []
          InterIndices: [4×2 double]
                  lpar: []
                  rpar: []
          LeftNotInter: [2 3]
         RightNotInter: [1×0 double]
              NormCons: 0.2479

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Cluster'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C990 - G1014 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
          LeftNotInter: []
         RightNotInter: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  9
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  9
pMakeMotifModelFromSSF:   3   Cluster Left  2  3  4  5 Right  8
pMakeMotifModelFromSSF:   4   Initial Left  6 Right  7
pMakeMotifModelFromSSF:   5  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   6   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_97273.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.4505
   -4.4505
   -7.4256

Timestamp 18-Jul-2025 22:49:05
pMakeSCFGModels: Making JAR3D model for motif group IL_97631.1, number 404 of 411
pMakeNodes starting loop:     a=4V9F|1|0|A|562 B=4V9F|1|0|U|595
  2 Basepair   562  595 AU cWW 
No need to probe because of interaction between a=4V9F|1|0|C|563 B=4V9F|1|0|C|594
  3 Basepair   563  594 CC bif 
No need to probe because of interaction between a=4V9F|1|0|G|564 B=4V9F|1|0|A|593
  4 Basepair   564  593 GA tSH 
pMakeNodes probe for inserts:  a=4V9F|1|0|A|565 B=4V9F|1|0|G|592
    Insertion on left  4V9F|1|0|A|565
pMakeNodesProbeForInsertions:  a 4V9F|1|0|A|566 interacts with 4V9F|1|0|G|592
pMakeNodesProbeForInsertions:  B 4V9F|1|0|G|592 interacts with 4V9F|1|0|A|566
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 4V9F|1|0|G|592 interacts with 4V9F|1|0|A|566
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=4V9F|1|0|A|566 B=4V9F|1|0|G|592
  5 Basepair   566  592 AG tHS 
No need to probe because of interaction between a=4V9F|1|0|U|567 B=4V9F|1|0|A|591
  6 Basepair   567  591 UA cWW 
  7 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   6  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   7   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4V9F|1|0|A|565
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A562 - U595 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'C'
               Comment: ' // Basepair C563 - C594 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GA'
           RightLetter: 'A'
               Comment: ' // Basepair G564 - A593 tSH '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4V9F|1|0|A|565'
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 5
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'G'
               Comment: ' // Basepair A566 - G592 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U567 - A591 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  9
pMakeMotifModelFromSSF:   5     Fixed Left  4 Right  8
pMakeMotifModelFromSSF:   6   Initial Left  5 Right  8
pMakeMotifModelFromSSF:   7  Basepair Left  5 Right  8
pMakeMotifModelFromSSF:   8  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   9   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_97631.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.0325

Timestamp 18-Jul-2025 22:49:05
pMakeSCFGModels: Making JAR3D model for motif group IL_97697.1, number 405 of 411
pMakeNodes starting loop:     a=5M0I|1|F|A|4 B=5M0I|1|F|U|22
  2 Basepair     4   22 AU cWW 
pMakeNodes probe for inserts:  a=5M0I|1|F|A|5 B=5M0I|1|F|A|20
    Insertion on left  5M0I|1|F|A|5
    Insertion on left  5M0I|1|F|C|6
    Insertion on left  5M0I|1|F|G|8
    Insertion on left  5M0I|1|F|A|9
    Insertion on right 5M0I|1|F|A|20
pMakeNodesProbeForInsertions:  a 5M0I|1|F|A|10 interacts with 5M0I|1|F|C|19
pMakeNodesProbeForInsertions:  B 5M0I|1|F|C|19 interacts with 5M0I|1|F|A|10
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5M0I|1|F|C|19 interacts with 5M0I|1|F|A|10
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=5M0I|1|F|A|10 B=5M0I|1|F|C|19
  3 Basepair    10   19 AC bif 
No need to probe because of interaction between a=5M0I|1|F|U|11 B=5M0I|1|F|A|18
  4 Basepair    11   18 UA cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:   5   Hairpin Left  8 Right  7
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5M0I|1|F|A|5
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5M0I|1|F|C|6
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5M0I|1|F|U|7
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5M0I|1|F|G|8
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 5M0I|1|F|C|19
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [11×11 double]
         Extensibility: [0 1 1 1 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 11
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'AACGA'
           RightLetter: 'AU'
               Comment: ' // Basepair A4 - U22 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5M0I|1|F|A|5'
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5M0I|1|F|C|6'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5M0I|1|F|U|7'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5M0I|1|F|G|8'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 5M0I|1|F|C|19'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 13
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 13

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 14
             LeftIndex: 6
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A10 - C19 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 14

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 15
             LeftIndex: 7
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U11 - A18 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 15

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 17
             LeftIndex: 8
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 8
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 11
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right 11
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right 10
pMakeMotifModelFromSSF:   4   Initial Left  3 Right 10
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right 10
pMakeMotifModelFromSSF:   6   Initial Left  4 Right 10
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right 10
pMakeMotifModelFromSSF:   8   Initial Left  5 Right 10
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right 10
pMakeMotifModelFromSSF:  10   Initial Left  6 Right 10
pMakeMotifModelFromSSF:  11     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:  12   Initial Left  6 Right  9
pMakeMotifModelFromSSF:  13  Basepair Left  6 Right  9
pMakeMotifModelFromSSF:  14  Basepair Left  7 Right  8
pMakeMotifModelFromSSF:  15   Hairpin Left  8 Right  7
pNextNodeJunction: Found a hairpin at node 15
pNextNodeJunction: Found a hairpin at node 15

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_97697.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.2338
   -7.2338
   -7.2338
   -7.2338

Timestamp 18-Jul-2025 22:49:05
pMakeSCFGModels: Making JAR3D model for motif group IL_98347.1, number 406 of 411
pMakeNodes starting loop:     a=6RTI|1|X|G|7||A B=6RTI|1|X|CFZ|37
  2 Basepair     7   37 GC cWW 
pMakeNodes probe for inserts:  a=6RTI|1|X|A|9||A B=6RTI|1|X|A|36
    Insertion on left  6RTI|1|X|A|9||A
    Insertion on left  6RTI|1|X|A|11
    Insertion on right 6RTI|1|X|A|36
pMakeNodesProbeForInsertions:  a 6RTI|1|X|A|12 interacts with 6RTI|1|X|UFT|35
pMakeNodesProbeForInsertions:  B 6RTI|1|X|UFT|35 interacts with 6RTI|1|X|A|12
pMakeNodesProbeForInsertions:  B 6RTI|1|X|UFT|35 interacts with 6RTI|1|X|A|12
pMakeNodes probed for insert:  a=6RTI|1|X|A|12 B=6RTI|1|X|UFT|35
  3 Basepair    12   35 AU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6RTI|1|X|A|36
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 6RTI|1|X|CFZ|37
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 6RTI|1|X|A|9||A
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAA'
           RightLetter: 'AC'
               Comment: ' // Basepair G7 - C37 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6RTI|1|X|A|36'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 6RTI|1|X|CFZ|37'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 6RTI|1|X|A|9||A'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A12 - U35 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_98347.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.7492

Timestamp 18-Jul-2025 22:49:06
pMakeSCFGModels: Making JAR3D model for motif group IL_99358.1, number 407 of 411
pMakeNodes starting loop:     a=4N0T|1|B|G|78 B=4N0T|1|B|C|68
  2 Basepair    78   68 GC cWW 
pMakeNodes probe for inserts:  a=4N0T|1|B|A|79 B=4N0T|1|B|C|67
    Insertion on left  4N0T|1|B|A|79
    Insertion on left  4N0T|1|B|U|80
    Insertion on right 4N0T|1|B|C|67
pMakeNodesProbeForInsertions:  a 4N0T|1|B|G|81 interacts with 4N0T|1|B|C|66
pMakeNodesProbeForInsertions:  B 4N0T|1|B|C|66 interacts with 4N0T|1|B|G|81
pMakeNodesProbeForInsertions:  B 4N0T|1|B|C|66 interacts with 4N0T|1|B|G|81
pMakeNodes probed for insert:  a=4N0T|1|B|G|81 B=4N0T|1|B|C|66
  3 Basepair    81   66 GC cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   4   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|C|67
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 4N0T|1|B|C|68
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 4N0T|1|B|U|80
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [7×7 double]
         Extensibility: [0 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.0082 0.0820 0.8197 0.0820 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GAU'
           RightLetter: 'CC'
               Comment: ' // Basepair G78 - C68 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|C|67'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 4N0T|1|B|C|68'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 4N0T|1|B|U|80'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 10
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G81 - C66 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 12
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  7
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  7
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  6
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  6
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  6
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  6
pMakeMotifModelFromSSF:   8   Initial Left  4 Right  5
pMakeMotifModelFromSSF:   9  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:  10   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 10
pNextNodeJunction: Found a hairpin at node 10

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_99358.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -7.1386
   -7.0981
   -7.0427
   -7.1513
   -7.5661
   -8.5864
   -8.8245
   -9.1320

Timestamp 18-Jul-2025 22:49:06
pMakeSCFGModels: Making JAR3D model for motif group IL_99380.1, number 408 of 411
pMakeNodes starting loop:     a=8CRE|1|CM|U|316 B=8CRE|1|CM|G|344
  2 Basepair   316  344 UG cWW 
pMakeNodes probe for inserts:  a=8CRE|1|CM|U|317 B=8CRE|1|CM|U|343
    Insertion on left  8CRE|1|CM|U|317
    Insertion on left  8CRE|1|CM|U|318
    Insertion on left  8CRE|1|CM|C|319
    Insertion on left  8CRE|1|CM|G|320
pMakeNodesProbeForInsertions:  a 8CRE|1|CM|A|321 interacts with 8CRE|1|CM|U|343
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|U|343 interacts with 8CRE|1|CM|A|321
pMakeNodesProbeForInsertions:  B 8CRE|1|CM|U|343 interacts with 8CRE|1|CM|A|321
pMakeNodes probed for insert:  a=8CRE|1|CM|A|321 B=8CRE|1|CM|U|343
  3 Basepair   321  343 AU cWW 
  4 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:   4   Hairpin Left  7 Right  6
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|U|317
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|U|318
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|C|319
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 8CRE|1|CM|G|320
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [8.1893e-05 8.1893e-04 0.0082 0.0819 0.8189 0.0819 0.0082]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9950 0.0045 5.0000e-04]
       rightLetterDist: [4×1 double]
            LeftLetter: 'UUUCG'
           RightLetter: 'G'
               Comment: ' // Basepair U316 - G344 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|U|317'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|U|318'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 8
             LeftIndex: 4
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|C|319'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 9
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 10
             LeftIndex: 5
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 8CRE|1|CM|G|320'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 10

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 11
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 11

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 12
             LeftIndex: 6
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A321 - U343 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 12

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 14
             LeftIndex: 7
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 7
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  4 Right  7
pMakeMotifModelFromSSF:   7     Fixed Left  4 Right  7
pMakeMotifModelFromSSF:   8   Initial Left  5 Right  7
pMakeMotifModelFromSSF:   9     Fixed Left  5 Right  7
pMakeMotifModelFromSSF:  10   Initial Left  6 Right  7
pMakeMotifModelFromSSF:  11  Basepair Left  6 Right  7
pMakeMotifModelFromSSF:  12   Hairpin Left  7 Right  6
pNextNodeJunction: Found a hairpin at node 12
pNextNodeJunction: Found a hairpin at node 12

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_99380.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -4.8115

Timestamp 18-Jul-2025 22:49:06
pMakeSCFGModels: Making JAR3D model for motif group IL_99498.1, number 409 of 411
pMakeNodes starting loop:     a=3IGI|1|A|G|10 B=3IGI|1|A|C|262
  2 Basepair    10  262 GC cWW 
pMakeNodes probe for inserts:  a=3IGI|1|A|C|11 B=3IGI|1|A|U|259
    Insertion on left  3IGI|1|A|C|11
    Insertion on right 3IGI|1|A|U|259
pMakeNodesProbeForInsertions:  a 3IGI|1|A|A|12 interacts with 3IGI|1|A|U|258
pMakeNodesProbeForInsertions:  B 3IGI|1|A|U|258 interacts with 3IGI|1|A|A|12
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 3IGI|1|A|U|258 interacts with 3IGI|1|A|A|12
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
pMakeNodes probed for insert:  a=3IGI|1|A|A|12 B=3IGI|1|A|U|258
  3 Basepair    12  258 AU tHW 
No need to probe because of interaction between a=3IGI|1|A|G|14 B=3IGI|1|A|C|257
  4 Basepair    14  257 GC cWW 
  5 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   4  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   5   Hairpin Left  5 Right  4
pMakeMotifModelFromSSF:  Adding an Initial node after a Basepair
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 3IGI|1|A|C|11
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the right for 3IGI|1|A|U|258
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
pMakeMotifModelFromSSF:  Removing Initial node after Basepair
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.0826 0.8264 0.0826 0.0083]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.0826 0.8264 0.0826 0.0083]
       rightLetterDist: [4×1 double]
            LeftLetter: 'GC'
           RightLetter: 'UC'
               Comment: ' // Basepair G10 - C262 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 3IGI|1|A|C|11'
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 6
             LeftIndex: 3
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: 1
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0 1]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on right for 3IGI|1|A|U|258'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 7
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: []
           RightLetter: []
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'U'
               Comment: ' // Basepair A12 - U258 tHW '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 9
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'C'
               Comment: ' // Basepair G14 - C257 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 9

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 11
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3     Fixed Left  2 Right  7
pMakeMotifModelFromSSF:   4   Initial Left  3 Right  7
pMakeMotifModelFromSSF:   5     Fixed Left  3 Right  7
pMakeMotifModelFromSSF:   6   Initial Left  3 Right  6
pMakeMotifModelFromSSF:   7  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   8  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   9   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 9
pNextNodeJunction: Found a hairpin at node 9

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_99498.1_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.1525

Timestamp 18-Jul-2025 22:49:06
pMakeSCFGModels: Making JAR3D model for motif group IL_99646.2, number 410 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|1437 B=5J7L|1|DA|G|1555
  2 Basepair  1437 1555 CG cWW 
No need to probe because of interaction between a=5J7L|1|DA|U|1438 B=5J7L|1|DA|A|1553
  3 Basepair  1438 1553 UA tWH 
No need to probe because of interaction between a=5J7L|1|DA|A|1439 B=5J7L|1|DA|A|1552
  4 Basepair  1439 1552 AA tHS 
No need to probe because of interaction between a=5J7L|1|DA|U|1440 B=5J7L|1|DA|A|1551
  5 Basepair  1440 1551 UA cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [8×8 double]
         Extensibility: [0 1 1 1 1 1 1 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 3
             LeftIndex: 1
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'C'
           RightLetter: 'G'
               Comment: ' // Basepair C1437 - G1555 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 4
             LeftIndex: 2
            RightIndex: 7
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1438 - A1553 tWH '
              NumLoops: []
                  Edge: 4
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 5
             LeftIndex: 3
            RightIndex: 6
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'A'
               Comment: ' // Basepair A1439 - A1552 tHS '
              NumLoops: []
                  Edge: 10
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 6
             LeftIndex: 4
            RightIndex: 5
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'U'
           RightLetter: 'A'
               Comment: ' // Basepair U1440 - A1551 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]
              NormCons: []

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 7
             LeftIndex: 5
            RightIndex: 4
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 5
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
                  lpar: []
                  rpar: []
              NormCons: 1

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right  8
pMakeMotifModelFromSSF:   2  Basepair Left  1 Right  8
pMakeMotifModelFromSSF:   3  Basepair Left  2 Right  7
pMakeMotifModelFromSSF:   4  Basepair Left  3 Right  6
pMakeMotifModelFromSSF:   5  Basepair Left  4 Right  5
pMakeMotifModelFromSSF:   6   Hairpin Left  5 Right  4
pNextNodeJunction: Found a hairpin at node 6
pNextNodeJunction: Found a hairpin at node 6

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_99646.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -6.8563
   -7.3671
   -6.5247
   -7.1352
   -6.6244
   -6.5247

Timestamp 18-Jul-2025 22:49:06
pMakeSCFGModels: Making JAR3D model for motif group IL_99692.2, number 411 of 411
pMakeNodes starting loop:     a=5J7L|1|DA|C|1043 B=5J7L|1|DA|G|1112
pMakeNodes making a cluster near strand break a=5J7L|1|DA|C|1043 B=5J7L|1|DA|G|1112
pMakeNodesCluster: amax is 8 bmin is 9, use_amax is 1
pMakeNodesCluster: Cluster goes from 1 to 5 and then 11 to 13
aa is 5 bb is 11
  2 Cluster   5J7L|1|DA|C|1043:5J7L|1|DA|A|1048 5J7L|1|DA|G|1110:5J7L|1|DA|G|1112
    LR Inter  5J7L|1|DA|A|1048 5J7L|1|DA|G|1110 tHS 
    LR Inter  5J7L|1|DA|C|1044 5J7L|1|DA|A|1111 tSS 
    LR Inter  5J7L|1|DA|G|1047 5J7L|1|DA|A|1111 tSH 
    LR Inter  5J7L|1|DA|C|1043 5J7L|1|DA|G|1112 cWW 
    LR Inter  5J7L|1|DA|A|1048 5J7L|1|DA|G|1112 tSS 
    Left  strand conserved insertion 5J7L|1|DA|C|1045 at position 3
pMakeNodesCluster a=6 B=10 at the end
pMakeNodesCluster a=6 B=10 at the end
pMakeNodes probe for inserts:  a=5J7L|1|DA|C|1049 B=5J7L|1|DA|C|1109
    Insertion on left  5J7L|1|DA|C|1049
pMakeNodesProbeForInsertions:  a 5J7L|1|DA|A|1050 interacts with 5J7L|1|DA|C|1109
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|1109 interacts with 5J7L|1|DA|A|1050
pMakeNodesProbeForInsertions:  Found that the interaction a makes contains a stem
pMakeNodesProbeForInsertions:  B 5J7L|1|DA|C|1109 interacts with 5J7L|1|DA|A|1050
pMakeNodesProbeForInsertions:  Found that the interaction B makes contains a stem
  3 Initial   1049 (1 insertion) and 1109 (0 insertion)
pMakeNodes probed for insert:  a=5J7L|1|DA|A|1050 B=5J7L|1|DA|C|1109
  4 Basepair  1050 1109 AC bif 
No need to probe because of interaction between a=5J7L|1|DA|G|1051 B=5J7L|1|DA|U|1108
  5 Basepair  1051 1108 GU cWW 
  6 Hairpin type *
pMakeMotifModelFromSSF:  Nodes before fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 11 12 13
pMakeMotifModelFromSSF:   3   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   4  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   5  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   6   Hairpin Left  9 Right  8
pMakeMotifModelFromSSF:  Replacing Initial with Fixed on the left for 5J7L|1|DA|A|1048
pMakeMotifModelFromSSF:  Adding an Initial node after Fixed
All nodes in detail
Node 1

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 2
             LeftIndex: 1
            RightIndex: 13
             Insertion: []
                    id: ''
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Initial node'
              NumLoops: []
                  Edge: [13×13 double]
         Extensibility: [0 0 0 0 0 1 1 1 1 1 0 0 0]
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: ''
                IBases: []
    InteractionComment: ''
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 2

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Cluster'
              nextnode: 3
             LeftIndex: [1 2 3 4 5]
            RightIndex: [11 12 13]
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: 'CCCGA'
           RightLetter: 'GAG'
               Comment: ' // Cluster node 5J7L|1|DA|C|1043:5J7L|1|DA|A|1048 and 5J7L|1|DA|G|1110:5J7L|1|DA|G|1112'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4×6 double]
                     Z: []
           MiddleIndex: []
                     P: [17×2 double]
                  PIns: [1.0000e-05 1.0000]
               subtype: []
                  Left: [1 2 3 4 5]
                 Right: [1 2 3]
      InsertionComment: []
                IBases: [6×2 double]
    InteractionComment: {1×6 cell}
      JunctionDeletion: []
          InterIndices: [6×2 double]
          LeftNotInter: 3
         RightNotInter: [1×0 double]
              NormCons: 0.0247
                  lpar: []
                  rpar: []

Node 3

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 4
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9000 0.1000]
        leftLetterDist: [4×1 double]
       rightLengthDist: [0.9000 0.1000]
       rightLetterDist: [4×1 double]
            LeftLetter: 'C'
           RightLetter: []
               Comment: ' // Initial node 5J7L|1|DA|C|1049 - 5J7L|1|DA|C|1109 from node '
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: []
                     Z: []
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: []
                  rpar: []

Node 4

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Fixed'
              nextnode: 5
             LeftIndex: 6
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0 1]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: 1
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: ''
           RightLetter: ''
               Comment: ' // Fixed node on left for 5J7L|1|DA|A|1048'
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 1.0000e-03
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 5

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Initial'
              nextnode: 6
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9999 1.0000e-04]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9999 1.0000e-04]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // New Initial node after Fixed node'
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 6

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 7
             LeftIndex: 7
            RightIndex: 10
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'A'
           RightLetter: 'C'
               Comment: ' // Basepair A1050 - C1109 bif '
              NumLoops: []
                  Edge: 13
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 7

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Basepair'
              nextnode: 8
             LeftIndex: 8
            RightIndex: 9
             Insertion: []
                    id: []
        leftLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
        leftLetterDist: [0.2500 0.2500 0.2500 0.2500]
       rightLengthDist: [0.9900 0.0099 4.9502e-05 1.6501e-07]
       rightLetterDist: [0.2500 0.2500 0.2500 0.2500]
            LeftLetter: 'G'
           RightLetter: 'U'
               Comment: ' // Basepair G1051 - U1108 cWW '
              NumLoops: []
                  Edge: 1
         Extensibility: []
                Delete: 0.0100
              SubsProb: [4×4 double]
                     Z: 1
           MiddleIndex: []
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: []
    InteractionComment: []
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: []
                  lpar: [17×1 double]
                  rpar: [17×1 double]

Node 8

ans = 

  <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> with fields:

                  type: 'Hairpin'
              nextnode: 9
             LeftIndex: 9
            RightIndex: 8
             Insertion: []
                    id: []
        leftLengthDist: []
        leftLetterDist: []
       rightLengthDist: []
       rightLetterDist: []
            LeftLetter: '*'
           RightLetter: ''
               Comment: ' // Hairpin node type *'
              NumLoops: []
                  Edge: []
         Extensibility: []
                Delete: []
              SubsProb: [5×5 double]
                     Z: []
           MiddleIndex: 9
                     P: []
                  PIns: []
               subtype: []
                  Left: []
                 Right: []
      InsertionComment: []
                IBases: [1 1]
    InteractionComment: {' // Hairpin for truncation'}
      JunctionDeletion: []
          InterIndices: []
          LeftNotInter: []
         RightNotInter: []
              NormCons: 1
                  lpar: []
                  rpar: []

pMakeMotifModelFromSSF:  Nodes after fixes
pMakeMotifModelFromSSF:   1   Initial Left  1 Right 13
pMakeMotifModelFromSSF:   2   Cluster Left  1  2  3  4  5 Right 11 12 13
pMakeMotifModelFromSSF:   3   Initial Left  6 Right 10
pMakeMotifModelFromSSF:   4     Fixed Left  6 Right 10
pMakeMotifModelFromSSF:   5   Initial Left  7 Right 10
pMakeMotifModelFromSSF:   6  Basepair Left  7 Right 10
pMakeMotifModelFromSSF:   7  Basepair Left  8 Right  9
pMakeMotifModelFromSSF:   8   Hairpin Left  9 Right  8
pNextNodeJunction: Found a hairpin at node 8
pNextNodeJunction: Found a hairpin at node 8

pMakeSCFGModels: Writing motif data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\lib\IL_99692.2_data.txt
pMakeSCFGModels: Calculating scores of sequences against their own model

OwnScores =

   -8.3762
   -7.8108
   -7.8837
   -7.9737
   -7.8837
   -8.2167

There are 411 motif groups, of which 323 are structured
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\IL\3.98\IL_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\IL\3.98\IL_GroupData.mat
pGenerateRandomMotifSequences: Unique sequence lengths:
     2     3
     2     4
     2     5
     2     6
     2     7
     2     8
     2     9
     2    10
     2    11
     2    12
     2    13
     2    14
     3     3
     3     4
     3     5
     3     6
     3     7
     3     8
     3     9
     3    10
     3    11
     3    12
     3    13
     3    14
     3    15
     3    16
     3    17
     4     4
     4     5
     4     6
     4     7
     4     8
     4     9
     4    10
     4    11
     4    12
     4    13
     4    14
     4    15
     4    16
     4    17
     4    22
     4    23
     5     5
     5     6
     5     7
     5     8
     5     9
     5    10
     5    11
     5    12
     5    13
     5    14
     5    15
     5    16
     5    17
     5    18
     5    21
     5    22
     5    23
     6     6
     6     7
     6     8
     6     9
     6    10
     6    11
     6    12
     6    13
     6    14
     6    15
     6    16
     6    17
     6    18
     6    21
     6    22
     7     7
     7     8
     7     9
     7    10
     7    11
     7    12
     7    13
     7    14
     7    16
     7    17
     7    18
     8     8
     8     9
     8    10
     8    11
     8    12
     8    13
     8    14
     8    16
     8    17
     8    18
     9     9
     9    10
     9    11
     9    12
     9    14
     9    15
     9    17
     9    18
     9    19
    10    10
    10    11
    10    12
    10    13
    10    14
    10    15
    10    18
    10    19
    11    11
    11    12
    11    13
    11    14
    11    15
    12    14
    12    15
    12    16
    12    17
    13    15
    13    16
    13    17
    14    15
    14    16

pGenerateRandomMotifSequences: Size of unique seq lengths:

ans =

   127     2

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8531 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8326 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8244 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8531 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8243 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8503 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8361 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8466 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8186 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8583 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8587 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8595 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8138 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8562 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8320 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8546 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8617 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8236 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8565 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 8426 additional attempts to avoid the specified pairs
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\IL\3.98\IL_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\IL\3.98\IL_GroupData.mat
pGenerateRandomMotifSequences: Unique sequence lengths:
     2     3
     2     4
     2     5
     2     6
     2     7
     2     8
     2     9
     2    10
     2    11
     2    12
     2    13
     2    14
     3     3
     3     4
     3     5
     3     6
     3     7
     3     8
     3     9
     3    10
     3    11
     3    12
     3    13
     3    14
     3    15
     3    16
     3    17
     4     4
     4     5
     4     6
     4     7
     4     8
     4     9
     4    10
     4    11
     4    12
     4    13
     4    14
     4    15
     4    16
     4    17
     4    22
     4    23
     5     5
     5     6
     5     7
     5     8
     5     9
     5    10
     5    11
     5    12
     5    13
     5    14
     5    15
     5    16
     5    17
     5    18
     5    21
     5    22
     5    23
     6     6
     6     7
     6     8
     6     9
     6    10
     6    11
     6    12
     6    13
     6    14
     6    15
     6    16
     6    17
     6    18
     6    21
     6    22
     7     7
     7     8
     7     9
     7    10
     7    11
     7    12
     7    13
     7    14
     7    16
     7    17
     7    18
     8     8
     8     9
     8    10
     8    11
     8    12
     8    13
     8    14
     8    16
     8    17
     8    18
     9     9
     9    10
     9    11
     9    12
     9    14
     9    15
     9    17
     9    18
     9    19
    10    10
    10    11
    10    12
    10    13
    10    14
    10    15
    10    18
    10    19
    11    11
    11    12
    11    13
    11    14
    11    15
    12    14
    12    15
    12    16
    12    17
    13    15
    13    16
    13    17
    14    15
    14    16

pGenerateRandomMotifSequences: Size of unique seq lengths:

ans =

   127     2

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5247 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5042 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5131 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5252 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5135 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 4937 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5058 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5150 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5063 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5052 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5200 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5139 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5064 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 4991 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5158 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 4977 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5078 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5177 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5025 additional attempts to avoid the specified pairs
pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: Generating 6350 sequences required 5145 additional attempts to avoid the specified pairs
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\IL\3.98\IL_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\IL\3.98\IL_GroupData.mat
pGenerateRandomMotifSequences: Unique sequence lengths:
     2     3
     2     4
     2     5
     2     6
     2     7
     2     8
     2     9
     2    10
     2    11
     2    12
     2    13
     2    14
     3     3
     3     4
     3     5
     3     6
     3     7
     3     8
     3     9
     3    10
     3    11
     3    12
     3    13
     3    14
     3    15
     3    16
     3    17
     4     4
     4     5
     4     6
     4     7
     4     8
     4     9
     4    10
     4    11
     4    12
     4    13
     4    14
     4    15
     4    16
     4    17
     4    22
     4    23
     5     5
     5     6
     5     7
     5     8
     5     9
     5    10
     5    11
     5    12
     5    13
     5    14
     5    15
     5    16
     5    17
     5    18
     5    21
     5    22
     5    23
     6     6
     6     7
     6     8
     6     9
     6    10
     6    11
     6    12
     6    13
     6    14
     6    15
     6    16
     6    17
     6    18
     6    21
     6    22
     7     7
     7     8
     7     9
     7    10
     7    11
     7    12
     7    13
     7    14
     7    16
     7    17
     7    18
     8     8
     8     9
     8    10
     8    11
     8    12
     8    13
     8    14
     8    16
     8    17
     8    18
     9     9
     9    10
     9    11
     9    12
     9    14
     9    15
     9    17
     9    18
     9    19
    10    10
    10    11
    10    12
    10    13
    10    14
    10    15
    10    18
    10    19
    11    11
    11    12
    11    13
    11    14
    11    15
    12    14
    12    15
    12    16
    12    17
    13    15
    13    16
    13    17
    14    15
    14    16

pGenerateRandomMotifSequences: Size of unique seq lengths:

ans =

   127     2

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pMakeRandomSequencesWeighted: using passed in sequence dimensions
pMakeRandomSequencesWeighted: dim variable columns 1 to 10
     2     2     2     2     2     2     2     2     2     2
     3     3     3     3     3     3     3     3     3     3

pMakeRandomSequencesWeighted: cWW distribution, initial letter distribution, transition matrix    0.2983
    0.3419
    0.1070
    0.1248
    0.0540
    0.0741

    0.2609
    0.1476
    0.3543
    0.2372

    0.4207    0.1605    0.2329    0.1860
    0.3400    0.2289    0.2593    0.1719
    0.4248    0.1662    0.2063    0.2027
    0.3940    0.1231    0.2851    0.1978

pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\IL\3.98\IL_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\IL\3.98\IL_GroupData.mat
Read random sequence variant file IL_RandomMotifSequences_1.fasta
max_rotation=1 r=0 n=1 a=GC*GAC FASTA(n).Sequence=GC*GAC
max_rotation=1 r=1 n=1 a=GAC*GC FASTA(n).Sequence=GC*GAC
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 22:49:28
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  13.5741 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  11.7248 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  11.4830 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  11.8795 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  11.5587 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  11.8662 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  11.7813 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  11.4392 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  12.7578 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  19.7926 minutes
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:09:23
Parsing 6350 sequences from file IL_RandomMotifSequences_1.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate  20.1448 minutes
Parsed against  100 models so far, total time estimate  23.1195 minutes
Parsed against  150 models so far, total time estimate  22.5219 minutes
Parsed against  200 models so far, total time estimate  22.5030 minutes
Parsed against  250 models so far, total time estimate  22.6588 minutes
Parsed against  300 models so far, total time estimate  22.6374 minutes
Parsed against  350 models so far, total time estimate  22.5624 minutes
Parsed against  400 models so far, total time estimate  22.3899 minutes
Read random sequence variant file IL_RandomMotifSequences_2.fasta
max_rotation=1 r=0 n=1 a=UC*GGG FASTA(n).Sequence=UC*GGG
max_rotation=1 r=1 n=1 a=GGG*UC FASTA(n).Sequence=UC*GGG
pJAR3DFalsePositiveStudy Timestamp 18-Jul-2025 23:31:45
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  49.1177 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  42.7448 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  41.4712 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  43.0217 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  41.6789 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  42.6501 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  42.3520 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  41.0330 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  40.5267 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  43.8951 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 00:15:03
Parsing 6350 sequences from file IL_RandomMotifSequences_2.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate  18.3824 minutes
Parsed against  100 models so far, total time estimate  21.4359 minutes
Parsed against  150 models so far, total time estimate  20.8123 minutes
Parsed against  200 models so far, total time estimate  20.6070 minutes
Parsed against  250 models so far, total time estimate  20.5865 minutes
Parsed against  300 models so far, total time estimate  20.5765 minutes
Parsed against  350 models so far, total time estimate  20.5936 minutes
Parsed against  400 models so far, total time estimate  20.6515 minutes
Read random sequence variant file IL_RandomMotifSequences_3.fasta
max_rotation=1 r=0 n=1 a=AC*GGU FASTA(n).Sequence=AC*GGU
max_rotation=1 r=1 n=1 a=GGU*AC FASTA(n).Sequence=AC*GGU
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 00:35:38
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  40.0921 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  35.1174 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  34.6075 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  35.8869 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  35.5024 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  36.9248 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  36.6205 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  35.5196 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  35.0182 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  38.3278 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 01:13:28
Parsing 6350 sequences from file IL_RandomMotifSequences_3.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate  18.4976 minutes
Parsed against  100 models so far, total time estimate  21.5282 minutes
Parsed against  150 models so far, total time estimate  21.0303 minutes
Parsed against  200 models so far, total time estimate  20.8111 minutes
Parsed against  250 models so far, total time estimate  20.7644 minutes
Parsed against  300 models so far, total time estimate  20.7606 minutes
Parsed against  350 models so far, total time estimate  20.7673 minutes
Parsed against  400 models so far, total time estimate  20.8554 minutes
Read random sequence variant file IL_RandomMotifSequences_4.fasta
max_rotation=1 r=0 n=1 a=GC*GUU FASTA(n).Sequence=GC*GUU
max_rotation=1 r=1 n=1 a=GUU*GC FASTA(n).Sequence=GC*GUU
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 01:34:15
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  43.8214 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  37.9401 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  36.9892 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  38.4663 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  37.3618 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  38.3917 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  38.1836 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  36.9745 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  36.4331 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  39.8438 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 02:13:36
Parsing 6350 sequences from file IL_RandomMotifSequences_4.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate  18.4382 minutes
Parsed against  100 models so far, total time estimate  21.1702 minutes
Parsed against  150 models so far, total time estimate  20.8796 minutes
Parsed against  200 models so far, total time estimate  20.6944 minutes
Parsed against  250 models so far, total time estimate  20.6338 minutes
Parsed against  300 models so far, total time estimate  20.6108 minutes
Parsed against  350 models so far, total time estimate  20.5902 minutes
Parsed against  400 models so far, total time estimate  20.6638 minutes
Read random sequence variant file IL_RandomMotifSequences_5.fasta
max_rotation=1 r=0 n=1 a=CG*UGG FASTA(n).Sequence=CG*UGG
max_rotation=1 r=1 n=1 a=UGG*CG FASTA(n).Sequence=CG*UGG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 02:34:11
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  43.0122 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  37.0382 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  36.2082 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  37.6071 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  36.5665 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  37.4245 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  37.3393 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  36.0451 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  35.5306 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  39.0393 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 03:12:45
Parsing 6350 sequences from file IL_RandomMotifSequences_5.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate  18.6086 minutes
Parsed against  100 models so far, total time estimate  21.4364 minutes
Parsed against  150 models so far, total time estimate  20.9050 minutes
Parsed against  200 models so far, total time estimate  20.6905 minutes
Parsed against  250 models so far, total time estimate  20.6020 minutes
Parsed against  300 models so far, total time estimate  20.4959 minutes
Parsed against  350 models so far, total time estimate  20.5128 minutes
Parsed against  400 models so far, total time estimate  20.5931 minutes
Read random sequence variant file IL_RandomMotifSequences_6.fasta
max_rotation=1 r=0 n=1 a=GG*CGC FASTA(n).Sequence=GG*CGC
max_rotation=1 r=1 n=1 a=CGC*GG FASTA(n).Sequence=GG*CGC
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 03:33:15
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  43.2772 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  37.3247 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  36.3121 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  37.8690 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  36.6685 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  37.6869 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  37.4162 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  36.3780 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  35.9545 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  38.7440 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 04:11:29
Parsing 6350 sequences from file IL_RandomMotifSequences_6.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate  18.1811 minutes
Parsed against  100 models so far, total time estimate  20.9449 minutes
Parsed against  150 models so far, total time estimate  20.5431 minutes
Parsed against  200 models so far, total time estimate  20.4525 minutes
Parsed against  250 models so far, total time estimate  20.5194 minutes
Parsed against  300 models so far, total time estimate  20.5922 minutes
Parsed against  350 models so far, total time estimate  20.5682 minutes
Parsed against  400 models so far, total time estimate  20.6694 minutes
Read random sequence variant file IL_RandomMotifSequences_7.fasta
max_rotation=1 r=0 n=1 a=GC*GCC FASTA(n).Sequence=GC*GCC
max_rotation=1 r=1 n=1 a=GCC*GC FASTA(n).Sequence=GC*GCC
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 04:32:05
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  41.3110 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  36.1507 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  35.6243 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  37.1162 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  36.1269 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  37.6304 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  37.2440 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  36.1965 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  35.6949 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  39.2024 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 05:10:48
Parsing 6350 sequences from file IL_RandomMotifSequences_7.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate  18.9956 minutes
Parsed against  100 models so far, total time estimate  21.7991 minutes
Parsed against  150 models so far, total time estimate  21.1534 minutes
Parsed against  200 models so far, total time estimate  20.8562 minutes
Parsed against  250 models so far, total time estimate  20.8892 minutes
Parsed against  300 models so far, total time estimate  20.7803 minutes
Parsed against  350 models so far, total time estimate  20.7662 minutes
Parsed against  400 models so far, total time estimate  20.8583 minutes
Read random sequence variant file IL_RandomMotifSequences_8.fasta
max_rotation=1 r=0 n=1 a=UU*ACG FASTA(n).Sequence=UU*ACG
max_rotation=1 r=1 n=1 a=ACG*UU FASTA(n).Sequence=UU*ACG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 05:31:34
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  42.5954 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  37.3031 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  36.3550 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  37.6965 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  36.6202 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  37.7111 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  37.4631 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  36.4134 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  35.8947 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  39.4495 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 06:10:32
Parsing 6350 sequences from file IL_RandomMotifSequences_8.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate  18.5989 minutes
Parsed against  100 models so far, total time estimate  21.4125 minutes
Parsed against  150 models so far, total time estimate  20.9333 minutes
Parsed against  200 models so far, total time estimate  20.7011 minutes
Parsed against  250 models so far, total time estimate  20.7604 minutes
Parsed against  300 models so far, total time estimate  20.7276 minutes
Parsed against  350 models so far, total time estimate  20.7341 minutes
Parsed against  400 models so far, total time estimate  20.7873 minutes
Read random sequence variant file IL_RandomMotifSequences_9.fasta
max_rotation=1 r=0 n=1 a=GC*GGU FASTA(n).Sequence=GC*GGU
max_rotation=1 r=1 n=1 a=GGU*GC FASTA(n).Sequence=GC*GGU
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 06:31:14
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  42.4329 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  36.8661 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  36.0384 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  37.3789 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  36.3280 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  37.3662 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  37.1069 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  35.9709 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  35.5675 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  39.0278 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 07:09:48
Parsing 6350 sequences from file IL_RandomMotifSequences_9.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate  18.5765 minutes
Parsed against  100 models so far, total time estimate  21.3776 minutes
Parsed against  150 models so far, total time estimate  20.8161 minutes
Parsed against  200 models so far, total time estimate  20.6479 minutes
Parsed against  250 models so far, total time estimate  20.6535 minutes
Parsed against  300 models so far, total time estimate  20.6546 minutes
Parsed against  350 models so far, total time estimate  20.8195 minutes
Parsed against  400 models so far, total time estimate  20.9234 minutes
Read random sequence variant file IL_RandomMotifSequences_10.fasta
max_rotation=1 r=0 n=1 a=UA*UAA FASTA(n).Sequence=UA*UAA
max_rotation=1 r=1 n=1 a=UAA*UA FASTA(n).Sequence=UA*UAA
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 07:30:39
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  42.7598 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  36.9974 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  36.2171 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  37.5683 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  36.4759 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  37.5848 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  37.3645 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  36.2073 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  35.7880 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  39.3590 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 08:09:32
Parsing 6350 sequences from file IL_RandomMotifSequences_10.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate  18.4588 minutes
Parsed against  100 models so far, total time estimate  21.4351 minutes
Parsed against  150 models so far, total time estimate  20.9652 minutes
Parsed against  200 models so far, total time estimate  20.7507 minutes
Parsed against  250 models so far, total time estimate  20.7765 minutes
Parsed against  300 models so far, total time estimate  20.7683 minutes
Parsed against  350 models so far, total time estimate  20.6971 minutes
Parsed against  400 models so far, total time estimate  20.7900 minutes
Read random sequence variant file IL_RandomMotifSequences_11.fasta
max_rotation=1 r=0 n=1 a=GG*CAC FASTA(n).Sequence=GG*CAC
max_rotation=1 r=1 n=1 a=CAC*GG FASTA(n).Sequence=GG*CAC
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 08:30:14
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  42.9051 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  37.1506 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  36.3974 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  37.6596 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  36.4517 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  37.3809 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  37.2078 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  36.1410 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  35.6337 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  39.0434 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 09:08:48
Parsing 6350 sequences from file IL_RandomMotifSequences_11.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate  18.4566 minutes
Parsed against  100 models so far, total time estimate  21.3848 minutes
Parsed against  150 models so far, total time estimate  20.8385 minutes
Parsed against  200 models so far, total time estimate  20.6542 minutes
Parsed against  250 models so far, total time estimate  20.6186 minutes
Parsed against  300 models so far, total time estimate  20.6818 minutes
Parsed against  350 models so far, total time estimate  20.6457 minutes
Parsed against  400 models so far, total time estimate  20.7332 minutes
Read random sequence variant file IL_RandomMotifSequences_12.fasta
max_rotation=1 r=0 n=1 a=UG*UGA FASTA(n).Sequence=UG*UGA
max_rotation=1 r=1 n=1 a=UGA*UG FASTA(n).Sequence=UG*UGA
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 09:29:28
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  42.7248 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  36.7868 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  30.7416 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  26.5184 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  23.3586 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  21.8397 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  20.4414 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  19.1020 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  18.1931 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  18.6577 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 09:47:49
Parsing 6350 sequences from file IL_RandomMotifSequences_12.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate   8.7167 minutes
Parsed against  100 models so far, total time estimate  12.7032 minutes
Parsed against  150 models so far, total time estimate  15.4361 minutes
Parsed against  200 models so far, total time estimate  16.7196 minutes
Parsed against  250 models so far, total time estimate  17.6454 minutes
Parsed against  300 models so far, total time estimate  18.3663 minutes
Parsed against  350 models so far, total time estimate  18.8968 minutes
Parsed against  400 models so far, total time estimate  18.4621 minutes
Read random sequence variant file IL_RandomMotifSequences_13.fasta
max_rotation=1 r=0 n=1 a=CA*UCG FASTA(n).Sequence=CA*UCG
max_rotation=1 r=1 n=1 a=UCG*CA FASTA(n).Sequence=CA*UCG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 10:06:17
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  24.0122 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  17.1362 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  15.2051 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  14.8258 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  13.9971 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  14.0360 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  13.7369 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  13.2174 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  12.9274 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  13.8968 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 10:20:00
Parsing 6350 sequences from file IL_RandomMotifSequences_13.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate   8.6103 minutes
Parsed against  100 models so far, total time estimate   9.7654 minutes
Parsed against  150 models so far, total time estimate   9.5601 minutes
Parsed against  200 models so far, total time estimate   9.4466 minutes
Parsed against  250 models so far, total time estimate   9.4510 minutes
Parsed against  300 models so far, total time estimate   9.4390 minutes
Parsed against  350 models so far, total time estimate   9.4423 minutes
Parsed against  400 models so far, total time estimate   9.4634 minutes
Read random sequence variant file IL_RandomMotifSequences_14.fasta
max_rotation=1 r=0 n=1 a=GU*AGC FASTA(n).Sequence=GU*AGC
max_rotation=1 r=1 n=1 a=AGC*GU FASTA(n).Sequence=GU*AGC
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 10:29:26
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  14.1444 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  12.2300 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  11.9345 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  12.4241 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  12.0519 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  12.3360 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  12.2393 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  11.8757 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  11.7032 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  12.7465 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 10:42:02
Parsing 6350 sequences from file IL_RandomMotifSequences_14.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate   8.5288 minutes
Parsed against  100 models so far, total time estimate   9.6709 minutes
Parsed against  150 models so far, total time estimate   9.4430 minutes
Parsed against  200 models so far, total time estimate   9.3515 minutes
Parsed against  250 models so far, total time estimate   9.3548 minutes
Parsed against  300 models so far, total time estimate   9.3513 minutes
Parsed against  350 models so far, total time estimate   9.3585 minutes
Parsed against  400 models so far, total time estimate   9.3979 minutes
Read random sequence variant file IL_RandomMotifSequences_15.fasta
max_rotation=1 r=0 n=1 a=CG*CCG FASTA(n).Sequence=CG*CCG
max_rotation=1 r=1 n=1 a=CCG*CG FASTA(n).Sequence=CG*CCG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 10:51:24
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  14.0976 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  12.1773 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  11.8618 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  12.3157 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  11.9739 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  12.2982 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  12.2191 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  11.8796 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  11.7360 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  12.8020 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 11:04:03
Parsing 6350 sequences from file IL_RandomMotifSequences_15.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate   8.5662 minutes
Parsed against  100 models so far, total time estimate   9.6870 minutes
Parsed against  150 models so far, total time estimate   9.5065 minutes
Parsed against  200 models so far, total time estimate   9.4020 minutes
Parsed against  250 models so far, total time estimate   9.3954 minutes
Parsed against  300 models so far, total time estimate   9.3872 minutes
Parsed against  350 models so far, total time estimate   9.4002 minutes
Parsed against  400 models so far, total time estimate   9.4288 minutes
Read random sequence variant file IL_RandomMotifSequences_16.fasta
max_rotation=1 r=0 n=1 a=UG*UGG FASTA(n).Sequence=UG*UGG
max_rotation=1 r=1 n=1 a=UGG*UG FASTA(n).Sequence=UG*UGG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 11:13:27
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  14.0135 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  12.2579 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  11.9486 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  12.3839 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  12.0173 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  12.3463 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  12.2625 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  11.9214 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  11.7871 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  12.8695 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 11:26:10
Parsing 6350 sequences from file IL_RandomMotifSequences_16.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate   8.5489 minutes
Parsed against  100 models so far, total time estimate   9.7087 minutes
Parsed against  150 models so far, total time estimate   9.4734 minutes
Parsed against  200 models so far, total time estimate   9.3770 minutes
Parsed against  250 models so far, total time estimate   9.3879 minutes
Parsed against  300 models so far, total time estimate   9.3768 minutes
Parsed against  350 models so far, total time estimate   9.3801 minutes
Parsed against  400 models so far, total time estimate   9.4116 minutes
Read random sequence variant file IL_RandomMotifSequences_17.fasta
max_rotation=1 r=0 n=1 a=GG*CUU FASTA(n).Sequence=GG*CUU
max_rotation=1 r=1 n=1 a=CUU*GG FASTA(n).Sequence=GG*CUU
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 11:35:33
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  13.8533 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  12.0123 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  11.7398 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  12.1931 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  11.8435 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  12.1724 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  12.0990 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  11.7654 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  11.6298 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  12.6889 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 11:48:05
Parsing 6350 sequences from file IL_RandomMotifSequences_17.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate   8.5589 minutes
Parsed against  100 models so far, total time estimate   9.6953 minutes
Parsed against  150 models so far, total time estimate   9.4864 minutes
Parsed against  200 models so far, total time estimate   9.3898 minutes
Parsed against  250 models so far, total time estimate   9.3871 minutes
Parsed against  300 models so far, total time estimate   9.3813 minutes
Parsed against  350 models so far, total time estimate   9.3975 minutes
Parsed against  400 models so far, total time estimate   9.4198 minutes
Read random sequence variant file IL_RandomMotifSequences_18.fasta
max_rotation=1 r=0 n=1 a=UU*AUG FASTA(n).Sequence=UU*AUG
max_rotation=1 r=1 n=1 a=AUG*UU FASTA(n).Sequence=UU*AUG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 11:57:28
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  13.8671 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  12.0112 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  11.7675 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  12.2359 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  11.9021 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  12.2414 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  12.1677 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  11.8301 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  11.6964 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  12.7643 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 12:10:05
Parsing 6350 sequences from file IL_RandomMotifSequences_18.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate   8.6004 minutes
Parsed against  100 models so far, total time estimate   9.7147 minutes
Parsed against  150 models so far, total time estimate   9.4825 minutes
Parsed against  200 models so far, total time estimate   9.3779 minutes
Parsed against  250 models so far, total time estimate   9.3929 minutes
Parsed against  300 models so far, total time estimate   9.4040 minutes
Parsed against  350 models so far, total time estimate   9.4143 minutes
Parsed against  400 models so far, total time estimate   9.4392 minutes
Read random sequence variant file IL_RandomMotifSequences_19.fasta
max_rotation=1 r=0 n=1 a=GU*AGC FASTA(n).Sequence=GU*AGC
max_rotation=1 r=1 n=1 a=AGC*GU FASTA(n).Sequence=GU*AGC
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 12:19:30
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  16.9259 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  14.5899 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  14.3202 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  14.9555 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  14.5374 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  14.9567 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  14.8842 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  14.4441 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  14.2678 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  15.4877 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 12:34:45
Parsing 6350 sequences from file IL_RandomMotifSequences_19.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate   8.5456 minutes
Parsed against  100 models so far, total time estimate   9.6668 minutes
Parsed against  150 models so far, total time estimate   9.4666 minutes
Parsed against  200 models so far, total time estimate   9.3627 minutes
Parsed against  250 models so far, total time estimate   9.3804 minutes
Parsed against  300 models so far, total time estimate   9.3611 minutes
Parsed against  350 models so far, total time estimate   9.3741 minutes
Parsed against  400 models so far, total time estimate   9.4033 minutes
Read random sequence variant file IL_RandomMotifSequences_20.fasta
max_rotation=1 r=0 n=1 a=CC*GAG FASTA(n).Sequence=CC*GAG
max_rotation=1 r=1 n=1 a=GAG*CC FASTA(n).Sequence=CC*GAG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 12:44:08
Finding core edit distance of 6350 sequences against  411 models over    2 rotations
pJAR3DFalsePositiveStudy: Checked edit distances for   40 models so far, total time estimate  13.9060 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for   80 models so far, total time estimate  12.0423 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  120 models so far, total time estimate  11.7466 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  160 models so far, total time estimate  12.2127 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  200 models so far, total time estimate  11.8788 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  240 models so far, total time estimate  12.2078 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  280 models so far, total time estimate  12.1489 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  320 models so far, total time estimate  11.8074 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  360 models so far, total time estimate  11.6735 minutes
pJAR3DFalsePositiveStudy: Checked edit distances for  400 models so far, total time estimate  12.7276 minutes
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 12:56:42
Parsing 6350 sequences from file IL_RandomMotifSequences_20.fasta against 411 models over 2 rotations
Parsed against   50 models so far, total time estimate   8.4784 minutes
Parsed against  100 models so far, total time estimate   9.6471 minutes
Parsed against  150 models so far, total time estimate   9.4643 minutes
Parsed against  200 models so far, total time estimate   9.3544 minutes
Parsed against  250 models so far, total time estimate   9.3731 minutes
Parsed against  300 models so far, total time estimate   9.3693 minutes
Parsed against  350 models so far, total time estimate   9.3858 minutes
Parsed against  400 models so far, total time estimate   9.4118 minutes
pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\IL\3.98\IL_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\IL\3.98\IL_GroupData.mat
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_1.mat
max_rotation=1 r=0 n=1 a=GC*GAC FASTA(n).Sequence=GC*GAC
max_rotation=1 r=1 n=1 a=GAC*GC FASTA(n).Sequence=GC*GAC
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:08
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_2.mat
max_rotation=1 r=0 n=1 a=UC*GGG FASTA(n).Sequence=UC*GGG
max_rotation=1 r=1 n=1 a=GGG*UC FASTA(n).Sequence=UC*GGG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:10
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_3.mat
max_rotation=1 r=0 n=1 a=AC*GGU FASTA(n).Sequence=AC*GGU
max_rotation=1 r=1 n=1 a=GGU*AC FASTA(n).Sequence=AC*GGU
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:10
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_4.mat
max_rotation=1 r=0 n=1 a=GC*GUU FASTA(n).Sequence=GC*GUU
max_rotation=1 r=1 n=1 a=GUU*GC FASTA(n).Sequence=GC*GUU
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:11
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_5.mat
max_rotation=1 r=0 n=1 a=CG*UGG FASTA(n).Sequence=CG*UGG
max_rotation=1 r=1 n=1 a=UGG*CG FASTA(n).Sequence=CG*UGG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:12
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_6.mat
max_rotation=1 r=0 n=1 a=GG*CGC FASTA(n).Sequence=GG*CGC
max_rotation=1 r=1 n=1 a=CGC*GG FASTA(n).Sequence=GG*CGC
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:12
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_7.mat
max_rotation=1 r=0 n=1 a=GC*GCC FASTA(n).Sequence=GC*GCC
max_rotation=1 r=1 n=1 a=GCC*GC FASTA(n).Sequence=GC*GCC
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:13
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_8.mat
max_rotation=1 r=0 n=1 a=UU*ACG FASTA(n).Sequence=UU*ACG
max_rotation=1 r=1 n=1 a=ACG*UU FASTA(n).Sequence=UU*ACG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:14
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_9.mat
max_rotation=1 r=0 n=1 a=GC*GGU FASTA(n).Sequence=GC*GGU
max_rotation=1 r=1 n=1 a=GGU*GC FASTA(n).Sequence=GC*GGU
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:14
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_10.mat
max_rotation=1 r=0 n=1 a=UA*UAA FASTA(n).Sequence=UA*UAA
max_rotation=1 r=1 n=1 a=UAA*UA FASTA(n).Sequence=UA*UAA
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:15
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_11.mat
max_rotation=1 r=0 n=1 a=GG*CAC FASTA(n).Sequence=GG*CAC
max_rotation=1 r=1 n=1 a=CAC*GG FASTA(n).Sequence=GG*CAC
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:15
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_12.mat
max_rotation=1 r=0 n=1 a=UG*UGA FASTA(n).Sequence=UG*UGA
max_rotation=1 r=1 n=1 a=UGA*UG FASTA(n).Sequence=UG*UGA
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:16
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_13.mat
max_rotation=1 r=0 n=1 a=CA*UCG FASTA(n).Sequence=CA*UCG
max_rotation=1 r=1 n=1 a=UCG*CA FASTA(n).Sequence=CA*UCG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:17
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_14.mat
max_rotation=1 r=0 n=1 a=GU*AGC FASTA(n).Sequence=GU*AGC
max_rotation=1 r=1 n=1 a=AGC*GU FASTA(n).Sequence=GU*AGC
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:17
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_15.mat
max_rotation=1 r=0 n=1 a=CG*CCG FASTA(n).Sequence=CG*CCG
max_rotation=1 r=1 n=1 a=CCG*CG FASTA(n).Sequence=CG*CCG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:18
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_16.mat
max_rotation=1 r=0 n=1 a=UG*UGG FASTA(n).Sequence=UG*UGG
max_rotation=1 r=1 n=1 a=UGG*UG FASTA(n).Sequence=UG*UGG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:18
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_17.mat
max_rotation=1 r=0 n=1 a=GG*CUU FASTA(n).Sequence=GG*CUU
max_rotation=1 r=1 n=1 a=CUU*GG FASTA(n).Sequence=GG*CUU
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:19
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_18.mat
max_rotation=1 r=0 n=1 a=UU*AUG FASTA(n).Sequence=UU*AUG
max_rotation=1 r=1 n=1 a=AUG*UU FASTA(n).Sequence=UU*AUG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:20
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_19.mat
max_rotation=1 r=0 n=1 a=GU*AGC FASTA(n).Sequence=GU*AGC
max_rotation=1 r=1 n=1 a=AGC*GU FASTA(n).Sequence=GU*AGC
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:20
Evaluating how sequences fit models
Loaded false positive study data file C:\Users\zirbel\Documents\JAR3D\IL\3.98\diagnostic\IL_RandomMotifSequences_20.mat
max_rotation=1 r=0 n=1 a=CC*GAG FASTA(n).Sequence=CC*GAG
max_rotation=1 r=1 n=1 a=GAG*CC FASTA(n).Sequence=CC*GAG
pJAR3DFalsePositiveStudy Timestamp 19-Jul-2025 13:06:21
Evaluating how sequences fit models
Saved group data

GroupData = 

  1×411 <a href="matlab:helpPopup struct" style="font-weight:bold">struct</a> array with fields:

    MotifID
    Signature
    NumNT
    NumBasepairs
    Structured
    NumStacks
    NumBPh
    NumBR
    NumInstances
    Truncate
    NumFixed
    OwnScore
    OwnSequence
    DeficitCoeff
    CoreEditCoeff
    SequenceLengths
    MeanSequenceLength
    DeficitEditData

pGetModelData: loading C:\Users\zirbel\Documents\JAR3D\IL\3.98\IL_GroupData.mat
Loaded GroupData from C:\Users\zirbel\Documents\JAR3D\IL\3.98\IL_GroupData.mat
